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423 changed files with 1254710 additions and 46 deletions
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+/jupyterhub_volumes/course/data/Genbank
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-
+/web_src/**/*.RData
+/web_src/**/*.pdf
+/web_src/**/*_files
+/web_src/**/*_cache
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+/sandbox
+*.log
+ncbitaxo_*
--- a/.vscode/ltex.hiddenFalsePositives.en-US.txt
+++ b/.vscode/ltex.hiddenFalsePositives.en-US.txt
@@ -0,0 +1 @@
+{"rule":"MORFOLOGIK_RULE_EN_US","sentence":"^\\QA password that secures access to the system\nA user number or UID (User IDentifier) that identifies the user on the machine\nA location on the hard disk to store the user's files, called Home or home\nA group of users, which allows working in groups on the machine (see later)\\E$"}
--- a/fish-primers.qmd
+++ b/fish-primers.qmd
@@ -0,0 +1,862 @@
+---
+title: "Designing Fish primers"
+format: revealjs
+editor: visual
+---
+
+```{r setup, include=FALSE}
+library(knitr)
+```
+
+# Preparing the data
+
+------------------------------------------------------------------------
+
+## What do we need ?
+
+To design a new animal DNA metabarcode we download from the NCBI the following data
+
+-   The complete set of whole mitochondrial genomes
+-   The NCBI taxonomy
+
+------------------------------------------------------------------------
+
+## We need also:
+
+-   a Unix computer: a Mac or a Linux box
+-   A unix terminal window for typing commands
+-   Installed on the computer
+    -   The OBITools --- <http://github.com/metabarcoding/obitools4>
+    -   ecoPrimers --- <http://metabarcoding.org/ecoprimers>
+    -   R --- <http://wwww.r-project.org>
+
+------------------------------------------------------------------------
+
+## Downloading the mitochondrial genomes
+
+We can use an internet browser and download the files from NCBI FTP website
+
+![](ncbi-ftp.png){fig-align="center"}
+
+------------------------------------------------------------------------
+
+## Downloading the mitochondrial genomes
+
+We can use an internet browser and download the files from NCBI FTP website
+
+or run the following command lines
+
+```{bash}
+#| eval: false
+#| echo: true
+curl 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/mitochondrion/mitochondrion.1.genomic.gbff.gz' \
+     > mito.all.gb.gz
+```
+
+------------------------------------------------------------------------
+
+```{bash}
+#| eval: false
+#| echo: true
+zless mito.all.gb.gz
+```
+
+```         
+LOCUS       NW_009243181           45189 bp    DNA     linear   CON 06-OCT-2014
+DEFINITION  Fonticula alba strain ATCC 38817 mitochondrial scaffold
+            supercont2.211, whole genome shotgun sequence.
+ACCESSION   NW_009243181 NZ_AROH01000000
+VERSION     NW_009243181.1
+DBLINK      BioProject: PRJNA262900
+            Assembly: GCF_000388065.1
+KEYWORDS    WGS; RefSeq.
+SOURCE      mitochondrion Fonticula alba
+  ORGANISM  Fonticula alba
+            Eukaryota; Rotosphaerida; Fonticulaceae; Fonticula.
+REFERENCE   1  (bases 1 to 45189)
+```
+
+------------------------------------------------------------------------
+
+## Downloading the complete taxonomy
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy --download-ncbi
+```
+
+```         
+INFO[0000] Number of workers set 16                     
+INFO[0000] Downloading NCBI Taxdump to ncbitaxo_20250211.tgz 
+downloading 100% ████████████████████████████████████████| (66/66 MB, 5.1 MB/s)   
+```
+
+The NCBI taxonomy contains all the relationship between taxa. Each taxon is identified by a unique numerical id: `taxid`
+
+------------------------------------------------------------------------
+
+## The archive contains several files
+
+file: `nodes.dmp`
+
+```         
+1  |  1  |  no rank  |      |   8   |   0   | ...
+2   |   131567  |   superkingdom    |       |   0   |   0   |
+6   |   335928  |   genus   |       |   0   |   1   |
+7   |   6   |   species |   AC  |   0   |   1   |
+9   |   32199   |   species |   BA  |   0   |
+10  |   135621  |   genus   |       |   0   |
+11  |   1707    |   species |   CG  |   0   |   1   |
+13  |   203488  |   genus   |       |   0   |   1   |
+14  |   13  |   species |   DT  |   0   |   1   |
+```
+
+------------------------------------------------------------------------
+
+## file: `names.dmp`
+
+```         
+1   |   root    |       |   scientific name |
+2   |   Bacteria    |   Bacteria <prokaryote>   |   scientific name |
+2   |   Monera  |   Monera <Bacteria>   |   in-part |
+2   |   Procaryotae |   Procaryotae <Bacteria>  |   in-part |
+2   |   Prokaryota  |   Prokaryota <Bacteria>   |   in-part |
+2   |   Prokaryotae |   Prokaryotae <Bacteria>  |   in-part |
+2   |   bacteria    |   bacteria <blast2>   |   blast name  |
+2   |   eubacteria  |       |   genbank common name |
+2   |   prokaryote  |   prokaryote <Bacteria>   |   in-part |
+...
+10  |   Cellvibrio  |       |   scientific name |
+11  |   [Cellvibrio] gilvus |       |   scientific name |
+13  |   Dictyoglomus    |       |   scientific name |
+14  |   Dictyoglomus thermophilum   |       |   scientific name |
+```
+
+------------------------------------------------------------------------
+
+## Preparing the set of complete genomes
+
+```{bash}
+#| eval: false
+#| echo: true
+obiconvert --skip-empty \
+           --update-taxid \
+           -t ncbitaxo_20250211.tgz \
+           mito.all.gb.gz \
+       > mito.all.fasta
+head -5 mito.all.fasta
+```
+
+five first lines of the new `mito.all.fasta` file
+
+```         
+>NC_072933 {"definition":"Echinosophora koreensis mitochondrion, complete genome.","scientific_name":"mitochondrion Echinosophora koreensis","taxid":228658}
+ctttcgggtcggaaatagaagatctggattagatcccttctcgatagctttagtcagagc
+tcatccctcgaaaaagggagtagtgagatgagaaaagggtgactagaatacggaaattca
+actagtgaagtcagatccgggaattccactattgaagttatccgtcttaggcttcaagca
+agctatctttcaaggaagtcagtctaagccctaagccaagatctgctttttgccagtcaa
+```
+
+------------------------------------------------------------------------
+
+## We want:
+
+-   annotate sequences by their species `taxid`
+-   keep a single genome per species
+-   extract only vertebrate genome
+
+------------------------------------------------------------------------
+
+## Looking for the **Vertebrata**'s taxid
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy -t ncbitaxo_20250211.tgz \
+              --fixed \
+              'vertebrata'
+```
+
+``` csv
+taxid,parent,taxonomic_rank,scientific_name
+taxon:1261581 [Vertebrata]@genus,taxon:2008651 [Polysiphonioideae]@subfamily,genus,Vertebrata
+taxon:7742 [Vertebrata]@clade,taxon:89593 [Craniata]@subphylum,clade,Vertebrata
+```
+
+------------------------------------------------------------------------
+
+## Looking for the **Vertebrata**'s taxid
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy -t ncbitaxo_20250211.tgz \
+              --fixed \
+              'vertebrata' \
+    | csvlook
+```
+
+``` csv
+| taxid                            | parent                                      | taxonomic_rank | scientific_name |
+| -------------------------------- | ------------------------------------------- | -------------- | --------------- |
+| taxon:1261581 [Vertebrata]@genus | taxon:2008651 [Polysiphonioideae]@subfamily | genus          | Vertebrata      |
+| taxon:7742 [Vertebrata]@clade    | taxon:89593 [Craniata]@subphylum            | clade          | Vertebrata      |
+```
+
+## A genus called **Vertebrata**
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy -t ncbitaxo_20250211.tgz \
+              -p 2008651 \
+      | csvlook
+```
+
+``` csv
+| taxid                                       | parent                                      | taxonomic_rank | scientific_name    |
+| ------------------------------------------- | ------------------------------------------- | -------------- | ------------------ |
+| taxon:2008651 [Polysiphonioideae]@subfamily | taxon:2803 [Rhodomelaceae]@family           | subfamily      | Polysiphonioideae  |
+| taxon:2803 [Rhodomelaceae]@family           | taxon:2802 [Ceramiales]@order               | family         | Rhodomelaceae      |
+| taxon:2802 [Ceramiales]@order               | taxon:2045261 [Rhodymeniophycidae]@subclass | order          | Ceramiales         |
+| taxon:2045261 [Rhodymeniophycidae]@subclass | taxon:2806 [Florideophyceae]@class          | subclass       | Rhodymeniophycidae |
+| taxon:2806 [Florideophyceae]@class          | taxon:2763 [Rhodophyta]@phylum              | class          | Florideophyceae    |
+| taxon:2763 [Rhodophyta]@phylum              | taxon:2759 [Eukaryota]@superkingdom         | phylum         | Rhodophyta         |
+| taxon:2759 [Eukaryota]@superkingdom         | taxon:131567 [cellular organisms]@no rank   | superkingdom   | Eukaryota          |
+| taxon:131567 [cellular organisms]@no rank   | taxon:1 [root]@no rank                      | no rank        | cellular organisms |
+| taxon:1 [root]@no rank                      | taxon:1 [root]@no rank                      | no rank        | root               |
+```
+
+------------------------------------------------------------------------
+
+## Reannotation and selection of the genomes
+
+```{bash}
+#| eval: false
+#| echo: true
+obiannotate -t ncbitaxo_20250211.tgz \
+            --with-taxon-at-rank=species \
+            mito.all.fasta | \
+  obiannotate -S 'ori_taxid=annotations.taxid' | \
+  obiannotate -S 'taxid=annotations.species_taxid' | \
+  obiuniq -c taxid > mito.one.fasta
+```
+
+------------------------------------------------------------------------
+
+## Species representation
+
+```{bash}
+#| eval: false
+#| echo: true
+
+obicsv -k taxid mito.one.fasta \
+     | tail -n +2 \
+     | sort \
+     | uniq -c \
+     | sort -nk1 \
+     | cut -w -f 2 \
+     | uplot count
+```
+
+```         
+     ┌                                        ┐ 
+   1 ┤■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 17769.0   
+   2 ┤ 90.0                                     
+   3 ┤ 17.0                                     
+   4 ┤ 5.0                                      
+   5 ┤ 4.0                                      
+   6 ┤ 2.0                                      
+   7 ┤ 1.0                                      
+     └                                        ┘ 
+```
+
+------------------------------------------------------------------------
+
+## Selection of the vertebrata genomes
+
+```{bash}
+#| eval: false
+#| echo: true
+
+obigrep -t ncbitaxo_20250211.tgz \
+        -r 7742 \
+        mito.one.fasta > mito.vert.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+
+obicount mito.vert.fasta \
+   | csvlook
+```
+
+```         
+| entities |           n |
+| -------- | ----------- |
+| variants |       7,822 |
+| reads    |       7,823 |
+| symbols  | 131,378,756 |
+```
+
+------------------------------------------------------------------------
+
+## Prepare data for ecoPrimers 1/3
+
+```{bash}
+#| eval: false
+#| echo: true
+mkdir ncbitaxo_20250211
+cd ncbitaxo_20250211
+tar zxvf ../ncbitaxo_20250211.tgz 
+cd ..
+```
+
+------------------------------------------------------------------------
+
+## Prepare data for ecoPrimers 2/3
+
+```{bash}
+#| eval: false
+#| echo: true
+obiconvert -O mito.vert.fasta > mito.vert.old.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+head -5 mito.vert.old.fasta
+```
+
+``` csv
+>NC_071784 taxid=taxon:2065826 [Sineleotris saccharae]@species; count=1; ori_taxid=taxon:2065826 [Sineleotris saccharae]@species; scientific_name=mitochondrion Sineleotris saccharae; species_name=Sineleotris saccharae; species_taxid=taxon:2065826 [Sineleotris saccharae]@species;  Sineleotris saccharae mitochondrion, complete genome.
+gctagcgtagcttaaccaaagcataacactgaagatgttaagatgggccctagaaagccc
+cgcaagcacaaaagcttggtcctggctttactatcagcttaggctaaacttacacatgca
+agtatccgcatccccgtgagaatgcccttaagctcccaccgctaacaggagtcaaggagc
+cggtatcaggcacaaccctgagttagcccacgacaccttgctcagccacacccccaaggg
+```
+
+------------------------------------------------------------------------
+
+## Prepare data for ecoPrimers 3/3
+
+```{bash}
+#| eval: false
+#| echo: true
+ecoPCRFormat -t ncbitaxo_20250211 \
+             -f \
+             -n vertebrata \
+             mito.vert.old.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+ls -l vertebrata*
+```
+
+```         
+-rw-r--r--@ 1 coissac  staff  260899785 Feb 11 11:53 vertabrata.ndx
+-rw-r--r--@ 1 coissac  staff        546 Feb 11 11:53 vertabrata.rdx
+-rw-r--r--@ 1 coissac  staff  121379751 Feb 11 11:53 vertabrata.tdx
+-rw-r--r--@ 1 coissac  staff   40446318 Feb 11 11:54 vertabrata_001.sdx
+```
+
+------------------------------------------------------------------------
+
+## Looking for the *Teleostei* `taxid`
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy -t ncbitaxo_20250211.tgz \
+              --fixed \
+              'Teleostei' \
+    | csvlook
+```
+
+``` csv
+| taxid                              | parent                             | taxonomic_rank | scientific_name |
+| ---------------------------------- | ---------------------------------- | -------------- | --------------- |
+| taxon:32443 [Teleostei]@infraclass | taxon:41665 [Neopterygii]@subclass | infraclass     | Teleostei       |
+```
+
+------------------------------------------------------------------------
+
+## Selecting the best primer pairs
+
+```{bash}
+#| eval: false
+#| echo: true
+ecoPrimers -d vertebrata \
+           -e 3 -3 2 \
+           -l 30 -L 150 \
+           -r 32443 \
+           -c > Teleostei.ecoprimers
+```
+
+-   Total pair count : 9407
+-   Total good pair count : 407
+
+------------------------------------------------------------------------
+
+```{bash}
+#| eval: false
+#| echo: true
+head -35 Teleostei.ecoprimers
+```
+
+``` csv
+#
+# ecoPrimer version 0.5
+# Rank level optimisation : species
+# max error count by oligonucleotide : 3
+#
+# Restricted to taxon:
+#     32443 : Teleostei (infraclass)
+#
+# strict primer quorum  : 0.70
+# example quorum        : 0.90
+# counterexample quorum : 0.10
+#
+# database : vertebrata
+# Database is constituted of  3909 examples        corresponding to  3876 species
+#                        and     0 counterexamples corresponding to     0 species
+#
+# amplifiat length between [30,150] bp
+# DB sequences are considered as circular
+# Pairs having specificity less than 0.60 will be ignored
+#
+     0  AGAGTGACGGGCGGTGTG      CGTCAGGTCGAGGTGTAG      62.8    42.4    57.5    34.1    12      11      GG      3864    0       0.988   3832    0       0.989   2731    0.713      134     146     138.22
+     1  CGTCAGGTCGAGGTGTAG      GAGTGACGGGCGGTGTGT      57.5    34.1    63.1    42.9    11      12      GG      3863    0       0.988   3831    0       0.988   2730    0.713      133     145     137.22
+     2  CGTCAGGTCGAGGTGTAG      GGGAGAGTGACGGGCGGT      57.5    34.1    64.5    37.0    11      13      GG      3811    0       0.975   3779    0       0.975   2689    0.712      137     149     141.22
+     3  CGTCAGGTCGAGGTGTAG      GGGGAGAGTGACGGGCGG      57.5    34.1    65.5    38.4    11      14      GG      3804    0       0.973   3772    0       0.973   2682    0.711      138     149     142.22
+     4  ACACCGCCCGTCACTCTC      ACCTTCCGGTACACTTAC      62.5    36.8    54.0    16.6    12      9       GG      3850    0       0.985   3818    0       0.985   2658    0.696      46      132     66.51
+     5  AACGTCAGGTCGAGGTGT      AGAGTGACGGGCGGTGTG      58.8    28.4    62.8    41.7    10      12      GG      3779    0       0.967   3746    0       0.966   2653    0.708      137     148     140.23
+     6  ACACCGCCCGTCACTCTC      CACCTTCCGGTACACTTA      62.5    36.8    54.0    16.6    12      9       GG      3846    0       0.984   3814    0       0.984   2654    0.696      47      133     67.51
+     7  AACGTCAGGTCGAGGTGT      GAGTGACGGGCGGTGTGT      58.8    28.4    63.1    42.1    10      12      GG      3778    0       0.966   3745    0       0.966   2652    0.708      136     147     139.23
+     8  ACCTTCCGGTACACTTAC      CACACCGCCCGTCACTCT      54.0    16.6    62.8    37.3    9       12      GG      3845    0       0.984   3813    0       0.984   2653    0.696      47      133     67.51
+     9  ACACCGCCCGTCACTCTC      TCCGGTACACTTACCATG      62.5    36.8    54.1    18.1    12      9       GG      3851    0       0.985   3819    0       0.985   2651    0.694      42      128     62.51
+    10  ACACCGCCCGTCACTCTC      CCGGTACACTTACCATGT      62.5    36.8    54.4    18.6    12      9       GG      3851    0       0.985   3819    0       0.985   2651    0.694      41      127     61.51
+    11  ACACCGCCCGTCACTCTC      CCAAGTGCACCTTCCGGT      62.5    36.8    60.7    28.9    12      11      GG      3837    0       0.982   3805    0       0.982   2650    0.696      54      140     74.51
+    12  ACACCGCCCGTCACTCTC      GCACCTTCCGGTACACTT      62.5    36.8    57.7    22.5    12      10      GG      3842    0       0.983   3810    0       0.983   2650    0.696      48      134     68.51
+    13  ACACCGCCCGTCACTCTC      CGGTACACTTACCATGTT      62.5    36.8    52.4    15.7    12      8       GG      3850    0       0.985   3818    0       0.985   2650    0.694      40      126     60.51
+    14  ACACCGCCCGTCACTCTC      CACTTACCATGTTACGAC      62.5    36.8    51.1    27.7    12      8       GG      3850    0       0.985   3817    0       0.985   2649    0.694      35      121     55.51
+```
+
+------------------------------------------------------------------------
+
+-   Primer ID : 11
+
+ 
+
+| Primer  | sequence           | tm max | tm min | GC count |
+|---------|--------------------|--------|--------|----------|
+| Forward | ACACCGCCCGTCACTCTC | 62.5   | 36.8   | 12       |
+| Reverse | CCAAGTGCACCTTCCGGT | 60.7   | 28.9   | 11       |
+
+ 
+
+-   amplifying 3837/3909 sequences\
+-   identify 2650/3876 Species
+-   Size ranging from 54bp to 140bp (mean: 74.75 bp)
+
+## Testing the new primer pair
+
+```{bash}
+#| eval: false
+#| echo: true
+obipcr --forward ACACCGCCCGTCACTCTC \
+       --reverse CCAAGTGCACCTTCCGGT \
+       -e 5 \
+       -l 30 -L 150 \
+       -c \
+       mito.vert.fasta \
+       > Teleostei_11.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+head Teleostei_11.fasta
+```
+
+``` csv
+>NC_022183_sub[925..998] {"count":1,"definition":"Acrossocheilus hemispinus mitochondrion, complete genome.","direction":"forward","forward_error":1,"forward_match":"acaccgcccgtcaccctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:356810 [Acrossocheilus hemispinus]@species","reverse_error":0,"reverse_match":"ccaagtgcaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Acrossocheilus hemispinus","species_name":"Acrossocheilus hemispinus","species_taxid":"taxon:356810 [Acrossocheilus hemispinus]@species","taxid":"taxon:356810 [Acrossocheilus hemispinus]@species"}
+cccgtcaaaatacaccaaaaatacttaatacaataacactaacaaggggaggcaagtcgt
+aacatggtaagtgt
+>NC_018560_sub[916..988] {"count":1,"definition":"Astatotilapia calliptera mitochondrion, complete genome.","direction":"forward","forward_error":0,"forward_match":"acaccgcccgtcactctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:8154 [Astatotilapia calliptera]@species","reverse_error":1,"reverse_match":"ccaagtacaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Astatotilapia calliptera (eastern happy)","species_name":"Astatotilapia calliptera","species_taxid":"taxon:8154 [Astatotilapia calliptera]@species","taxid":"taxon:8154 [Astatotilapia calliptera]@species"}
+cccaagccaacaacatcctataaataatacattttaccggtaaaggggaggcaagtcgta
+acatggtaagtgt
+>NC_056117_sub[923..997] {"count":1,"definition":"Pseudocrossocheilus tridentis mitochondrion, complete genome.","direction":"forward","forward_error":0,"forward_match":"acaccgcccgtcactctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species","reverse_error":0,"reverse_match":"ccaagtgcaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Pseudocrossocheilus tridentis","species_name":"Pseudocrossocheilus tridentis","species_taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species","taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species"}
+ccctgtcaaaaagcatcaaatatatataataaattagcaatgacaaggggaggcaagtcg
+taacacggtaagtgt
+>NC_045904_sub[919..997] {"count":1,"definition":"Eospalax fontanierii mitochondrion, complete genome.","direction":"forward","forward_error":1,"forward_match":"acaccgcccgtcgctctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:146134 [Eospalax fontanierii]@species","reverse_error":4,"reverse_match":"ccaagcacactttccagt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Eospalax fontanierii","species_name":"Eospalax fontanierii","species_taxid":"taxon:146134 [Eospalax fontanierii]@species","taxid":"taxon:146134 [Eospalax fontanierii]@species"}
+```
+
+------------------------------------------------------------------------
+
+convert the fasta file to csv
+
+```{bash}
+#| eval: false
+#| echo: true
+obicsv --auto -s -i Teleostei_11.fasta > Teleostei_11.csv
+```
+
+and display the begining of the table
+
+```{bash}
+#| eval: false
+#| echo: true
+head Teleostei_11.csv | csvlook
+```
+
+``` csv
+| id                        | count | direction | forward_error | forward_match      | forward_primer     | ori_taxid                                            | reverse_error | reverse_match      | reverse_primer     | scientific_name                                        | species_name                  | species_taxid                                        | taxid                                                | sequence                                                                        |
+| ------------------------- | ----- | --------- | ------------- | ------------------ | ------------------ | ---------------------------------------------------- | ------------- | ------------------ | ------------------ | ------------------------------------------------------ | ----------------------------- | ---------------------------------------------------- | ---------------------------------------------------- | ------------------------------------------------------------------------------- |
+| NC_022183_sub[925..998]   |  True | forward   |          True | acaccgcccgtcaccctc | ACACCGCCCGTCACTCTC | taxon:356810 [Acrossocheilus hemispinus]@species     |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Acrossocheilus hemispinus                | Acrossocheilus hemispinus     | taxon:356810 [Acrossocheilus hemispinus]@species     | taxon:356810 [Acrossocheilus hemispinus]@species     | cccgtcaaaatacaccaaaaatacttaatacaataacactaacaaggggaggcaagtcgtaacatggtaagtgt      |
+| NC_018560_sub[916..988]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:8154 [Astatotilapia calliptera]@species        |             1 | ccaagtacaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Astatotilapia calliptera (eastern happy) | Astatotilapia calliptera      | taxon:8154 [Astatotilapia calliptera]@species        | taxon:8154 [Astatotilapia calliptera]@species        | cccaagccaacaacatcctataaataatacattttaccggtaaaggggaggcaagtcgtaacatggtaagtgt       |
+| NC_056117_sub[923..997]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:887881 [Pseudocrossocheilus tridentis]@species |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Pseudocrossocheilus tridentis            | Pseudocrossocheilus tridentis | taxon:887881 [Pseudocrossocheilus tridentis]@species | taxon:887881 [Pseudocrossocheilus tridentis]@species | ccctgtcaaaaagcatcaaatatatataataaattagcaatgacaaggggaggcaagtcgtaacacggtaagtgt     |
+| NC_045904_sub[919..997]   |  True | forward   |          True | acaccgcccgtcgctctc | ACACCGCCCGTCACTCTC | taxon:146134 [Eospalax fontanierii]@species          |             4 | ccaagcacactttccagt | CCAAGTGCACCTTCCGGT | mitochondrion Eospalax fontanierii                     | Eospalax fontanierii          | taxon:146134 [Eospalax fontanierii]@species          | taxon:146134 [Eospalax fontanierii]@species          | ctcaagtacataaacttggatatattcttaataacccaacaaaaatattagaggagataagtcgtaacaaggtaagcat |
+| NC_018546_sub[916..987]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:30732 [Oryzias melastigma]@species             |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Oryzias melastigma (Indian medaka)       | Oryzias melastigma            | taxon:30732 [Oryzias melastigma]@species             | taxon:30732 [Oryzias melastigma]@species             | cccgacccattttaaaaattaaataaaagatttcaggaactaaggggaggcaagtcgtaacatggtaagtgt        |
+| NC_044151_sub[922..993]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:2597641 [Sicyopterus squamosissimus]@species   |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Sicyopterus squamosissimus (cling goby)  | Sicyopterus squamosissimus    | taxon:2597641 [Sicyopterus squamosissimus]@species   | taxon:2597641 [Sicyopterus squamosissimus]@species   | cccaaaacaaacacacacataaataagaaaaaatgaaaataaaggggaggcaagtcgtaacatggtaagtgt        |
+| NC_044152_sub[922..994]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:2597642 [Sicyopterus stiphodonoides]@species   |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Sicyopterus stiphodonoides (cling goby)  | Sicyopterus stiphodonoides    | taxon:2597642 [Sicyopterus stiphodonoides]@species   | taxon:2597642 [Sicyopterus stiphodonoides]@species   | cccaaaacaaacacacacataaataagaaaaaantgaaaataaaggggaggcaagtcgtaacatggtaagtgt       |
+| NC_026976_sub[1453..1531] |  True | forward   |          True | acaccgcccgtcactccc | ACACCGCCCGTCACTCTC | taxon:9545 [Macaca nemestrina]@species               |             1 | ccaagtgcaccttccagt | CCAAGTGCACCTTCCGGT | mitochondrion Macaca nemestrina (pig-tailed macaque)   | Macaca nemestrina             | taxon:9545 [Macaca nemestrina]@species               | taxon:9545 [Macaca nemestrina]@species               | ctcaaatatatttaaggaacatcttaactaaacgccctaatatttatatagaggggataagtcgtaacatggtaagtgt |
+| NC_031553_sub[921..995]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:643337 [Puntioplites proctozystron]@species    |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Puntioplites proctozystron               | Puntioplites proctozystron    | taxon:643337 [Puntioplites proctozystron]@species    | taxon:643337 [Puntioplites proctozystron]@species    | ccctgtcaaaacgcactaaaaatatctaatacaaaagcaccgacaaggggaggcaagtcgtaacacggtaagtgt     |
+```
+
+# We are now switching to R
+
+------------------------------------------------------------------------
+
+## Preparing our R session
+
+First we have to download the two follong libraries
+
+```{r}
+#| echo: true
+library(tidyverse)
+library(ggpubr)
+library(ROBITools4)
+```
+
+------------------------------------------------------------------------
+
+## Loading the data
+
+```{r}
+#| echo: true
+
+fish <- read_csv('Teleostei_11.csv', show_col_types = FALSE)
+taxo <- read_ncbi_taxdump('ncbitaxo_20250211')
+assign_default_taxonomy(taxo)
+```
+
+------------------------------------------------------------------------
+
+Looking for Teleostei taxid
+
+```{r}
+#| echo: true
+teleo_taxid <- ecofind('Teleostei')
+teleo_taxid
+```
+
+------------------------------------------------------------------------
+
+## Format taxids
+
+```{r}
+#| echo: true
+fish %>% mutate(
+  taxid = as_taxid(
+      as.integer(
+         str_split_fixed(
+            str_split_fixed(
+               taxid,pattern = " ", 
+               n = 2)[,1],
+            ":",
+            2)[,2]))
+   ) %>% 
+  as_tbl_obipcr() %>%
+  mutate(across(taxon(),
+                .names="category",
+                .fn=taxonomy_classifier(Teleostei = 32443))) %>%
+  group_by(category) %>%
+  mutate(weight = taxonomic_weights(taxid,taxo)) %>%
+  ungroup() -> fish
+```
+
+------------------------------------------------------------------------
+
+## The fish tibble
+
+```{r}
+#| echo: true
+head(fish,n = 4)
+```
+
+------------------------------------------------------------------------
+
+## Identifying which sequences belongs fish
+
+```{r}
+#| echo: true
+table(fish$category)
+```
+
+------------------------------------------------------------------------
+
+## Testing the conservation of the priming sites
+
+```{r}
+#| echo: true
+pssm_forward <- pssm(fish$forward_match,
+                    weights = fish$weight,
+                    categories = fish$category)
+
+pssm_reverse <- pssm(fish$reverse_match,
+                    weights = fish$weight,
+                    categories = fish$category) 
+```
+
+```{r}
+#| echo: true
+pssm_forward
+```
+
+------------------------------------------------------------------------
+
+## Rescaling the matrix as Shanon entropy
+
+$$
+H = - \sum_{i \in \{A,C,G,T\}} p_i \times \frac{\log(p_i)}{\log(2)}
+$$
+
+```{r}
+#| echo: true
+pssm_forward <- pssm_scale_shanon(pssm_forward)
+pssm_reverse <- pssm_scale_shanon(pssm_reverse)
+```
+
+------------------------------------------------------------------------
+
+## Display the rescaled matrix
+
+```{r}
+#| echo: true
+pssm_forward
+```
+
+------------------------------------------------------------------------
+
+## The DNA logo of our primer pair
+
+```{r}
+#| echo: true
+flogo <- ggbarcodelogo(pssm_forward) + 
+         xlab("Forward primer") + ylab("Bits")
+rlogo <- ggbarcodelogo(pssm_reverse) + 
+         xlab("Reverse primer") + ylab("Bits")
+
+ggarrange(flogo,rlogo,ncol=2) -> dnaplot
+
+dnaplot
+```
+
+------------------------------------------------------------------------
+
+## How many mismatches ?
+
+```{r}
+#| echo: true
+ggbarcodemistmatch(fish$forward_error,
+                   fish$reverse_error,
+                   otu=fish$species_name,
+                   categories=fish$category) + theme_minimal()
+```
+
+------------------------------------------------------------------------
+
+## Are we discriminate taxa ?
+
+```{r}
+#| echo: true
+with(fish %>% filter(category == "Teleostei"),
+     discriminated_at_rank(taxid, 
+                  c("species","genus","family","order"),
+                           sequence))
+```
+
+------------------------------------------------------------------------
+
+## How many sequences will provide information at rank ?
+
+```{r}
+#| echo: true
+with(fish %>% filter(category == "Teleostei"),
+     discriminant_at_rank(taxid, 
+                  c("species","genus","family","order"),
+                           sequence))
+```
+
+------------------------------------------------------------------------
+
+## Is it the same for *Cyprinidae* ?
+
+```{r}
+#| echo: true
+cyprinidae_taxid <- ecofind('Cyprinidae')
+cyprinidae_taxid
+```
+
+------------------------------------------------------------------------
+
+## Classify according to both categories
+
+```{r}
+#| echo: true
+fish %>% 
+  mutate(across(taxon(),
+                .names="category2",
+                .fn=taxonomy_classifier(Teleostei = 32443,
+                                        Cyprinidae = 7953))) -> fish
+
+table(fish$category2)
+```
+
+------------------------------------------------------------------------
+
+## Are we discriminate taxa ?
+
+```{r}
+#| echo: true
+with(fish %>% filter(category2 == "Cyprinidae"),
+     discriminated_at_rank(taxid, 
+                  c("species","genus"),
+                           sequence))
+```
+
+# Go back to unix
+
+## We run ecoPrimers and ecoPCR on the select primer pair
+
+```{bash}
+#| eval: false
+#| echo: true
+ecoPrimers -d vertebrata \
+           -e 3 -3 2 \
+           -l 30 -L 150 \
+           -r 7953 -c > Cyprinidae.ecoprimers
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+obipcr --forward ACGGCGTAAAGGGTGGTT \
+       --reverse TATCTAATCCCAGTTTGT \
+       -e 5 \
+       -l 30 -L 500 \
+       -c \
+       mito.vert.fasta \
+       > Cyprinidae_14.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+obicsv --auto -s -i  Cyprinidae_14.fasta >  Cyprinidae_14.csv
+```
+
+# Go back to R
+
+```{r}
+cyprinidae <- read_csv('Cyprinidae_14.csv', 
+                       show_col_types = FALSE) %>%
+  mutate(
+  taxid = as_taxid(
+      as.integer(
+         str_split_fixed(
+            str_split_fixed(
+               taxid,pattern = " ", 
+               n = 2)[,1],
+            ":",
+            2)[,2]))
+   ) %>% 
+  as_tbl_obipcr() %>%
+  mutate(across(taxon(),
+                .names="category",
+                .fn=taxonomy_classifier(Teleostei = 32443, 
+                                        Cyprinidae = 7953))) %>%
+  group_by(category) %>%
+  mutate(weight = taxonomic_weights(taxid,taxo)) %>%
+  ungroup()
+```
+
+------------------------------------------------------------------------
+
+## Identifying which sequences belongs fish and *Cyprinidae*
+
+```{r}
+#| echo: true
+table(cyprinidae$category)
+```
+
+------------------------------------------------------------------------
+
+## Looking for conservation
+
+```{r}
+#| echo: true
+pssm_forward <- pssm(cyprinidae$forward_match,
+                    weights = cyprinidae$weight,
+                    categories = cyprinidae$category) %>%
+  pssm_scale_shanon()
+
+pssm_reverse <- pssm(cyprinidae$reverse_match,
+                    weights = cyprinidae$weight,
+                    categories = cyprinidae$category) %>%
+  pssm_scale_shanon()
+```
+
+------------------------------------------------------------------------
+
+## Plot the new DNA logo
+
+```{r}
+flogo <- ggbarcodelogo(pssm_forward) + 
+         xlab("Forward primer") + ylab("Bits")
+rlogo <- ggbarcodelogo(pssm_reverse) + 
+         xlab("Reverse primer") + ylab("Bits")
+
+ggarrange(flogo,rlogo,ncol=2) -> dnaplot
+
+dnaplot
+```
+
+------------------------------------------------------------------------
+
+## How many mismatches ?
+
+```{r}
+#| echo: true
+ggbarcodemistmatch(cyprinidae$forward_error,
+                   cyprinidae$reverse_error,
+                   otu=cyprinidae$species_name,
+                   categories=cyprinidae$category) + theme_minimal()
+```
+
+------------------------------------------------------------------------
+
+## Are we discriminate *Cyprinidae* taxa ?
+
+```{r}
+#| echo: true
+with(cyprinidae %>% filter(category == "Cyprinidae"),
+     discriminated_at_rank(taxid, 
+                  c("species","genus"),
+                           sequence))
+```
--- a/jupyterhub_volumes/course/biodiversity_metrics_exercises.ipynb
+++ b/jupyterhub_volumes/course/biodiversity_metrics_exercises.ipynb
--- a/jupyterhub_volumes/course/data/Wolf_diet/R_stats.ipynb
+++ b/jupyterhub_volumes/course/data/Wolf_diet/R_stats.ipynb
--- a/jupyterhub_volumes/course/data/Wolf_diet/vert01_ref_db.fasta.gz
+++ b/jupyterhub_volumes/course/data/Wolf_diet/vert01_ref_db.fasta.gz
--- a/jupyterhub_volumes/course/data/Wolf_diet/wolf.ipynb
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf.ipynb
--- a/jupyterhub_volumes/course/data/Wolf_diet/wolf.pdf
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf.pdf
--- a/jupyterhub_volumes/course/data/Wolf_diet/wolf_F.fastq
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf_F.fastq
--- a/jupyterhub_volumes/course/data/Wolf_diet/wolf_R.fastq
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf_R.fastq
--- a/jupyterhub_volumes/course/data/Wolf_diet/wolf_data_wolf_diet_ngsfilter.csv
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf_data_wolf_diet_ngsfilter.csv
@@ -0,0 +1,8 @@
+@param,matching,strict
+@param,primer_mismatches,2
+@param,indels,false
+experiment,sample,sample_tag,forward_primer,reverse_primer
+wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
--- a/jupyterhub_volumes/course/data/ref_db_raw.fasta
+++ b/jupyterhub_volumes/course/data/ref_db_raw.fasta
--- a/jupyterhub_volumes/course/data/ref_db_raw.fasta.zip
+++ b/jupyterhub_volumes/course/data/ref_db_raw.fasta.zip
--- a/jupyterhub_volumes/course/unix_exercises_bash.ipynb
+++ b/jupyterhub_volumes/course/unix_exercises_bash.ipynb
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@@ -115,6 +115,7 @@
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+            <li><a href="/obidoc/" target="_blank">OBITools 4 Doc</a></li>
            <li><a href="/jupyter/" target="_blank">JupyterHub</a></li>
            <li><a href="/sftp/" target="_blank">Data Admin</a></li>
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--- a/jupyterhub_volumes/web/obidoc/docs/about/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/about/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/advanced/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/advanced/index.html
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+  <channel>
+    <title>Advanced tools on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/advanced/</link>
+    <description>Recent content in Advanced tools on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/advanced/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.html
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+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.xml
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+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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+    <title>Sequence alignments on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/alignments/</link>
+    <description>Recent content in Sequence alignments on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.xml
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+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Exact alignment on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/alignments/obipairing/exact-alignment/</link>
+    <description>Recent content in Exact alignment on OBITools4 documentation</description>
+    <generator>Hugo</generator>
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--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/match.json
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/match.json
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/mismatch.json
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/mismatch.json
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/pairing_score.qmd
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/pairing_score.qmd
@@ -0,0 +1,149 @@
+---
+title: "Untitled"
+format: html
+editor: visual
+---
+
+```{r}
+library(tidyverse)
+library(plotly)
+library(matrixStats)
+```
+
+```{r}
+log_sum_exp <- function(a,b) {
+  m <- map2_dbl(a,b,max)
+  m + log(exp(a-m)+exp(b-m))
+}
+```
+
+$$
+\log(1 - e^b) = \log\left(-e^{(1-b)}\right)
+$$
+
+```{r}
+log1m_exp <- function(b) {
+  if (any(b >= 0)) {
+    stop(glue::glue("b must be negative (b={b})"))
+  }
+  return(log(-expm1(b)))  # expm1(b) = exp(b) - 1, pour éviter les erreurs d'arrondi
+}
+```
+
+$$
+\log(e^a - e^b) = a + \log(1 - e^{b-a})
+$$
+
+```{r}
+log_diff_exp <- function(a, b) {
+  # Vérifier si a > b pour éviter des résultats indéfinis
+  if (any(a < b)) {
+    stop(glue::glue("Erreur : a ({a}) doit etre strictement sup<75>rieur <20> b ({b}) pour que e^a - e^b soit positif."))
+  }
+  
+  # Calculer log(e^a - e^b) de manière stable
+  ifelse(a == b, -Inf,a + log1m_exp(b-a))
+}
+```
+
+$$
+P_{error} = 10^{-\frac{Q}{10}}
+$$
+
+$$
+\begin{aligned}
+q_F &= -\frac{Q_F}{10} \cdot \log(10) \\
+q_R &= -\frac{Q_R}{10} \cdot \log(10) \\ 
+P(macth | Obs(match)) &= (1-e^{q_F}) (1-e^{q_R}) + (1-e^{q_F})\frac{e^{q_R}}{4}+ (1-e^{q_R})\frac{e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
+&=1 - e^{q_R} - e^{q_F} + e^{q_F+q_R} + \frac{e^{q_R}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F+q_R}}{4} \\
+&= \frac{4 - 4e^{q_F} - 4e^{q_R} + 4e^{q_F+q_R} + e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4} \\
+&= \frac{4 - 3e^{q_F}- 3e^{q_R} + 3e^{q_F+q_R}}{4}\\
+&= \frac{4 - 3(e^{q_F}+e^{q_R}-e^{q_F+q_R})}{4} \\
+&= 1 - \frac{3}{4}\left(e^{q_F}+e^{q_R}-e^{q_F+q_R}\right)
+\end{aligned}
+$$
+
+```{r}
+Pm_match_observed <- function(Q_F, Q_R) {
+  l10 <- log(10)
+  l3 <- log(3)
+  l4 <- log(4)
+
+  q_F <- -Q_F/10*l10
+  q_R <- -Q_R/10*l10
+  
+  term1 <- log_sum_exp(q_F,q_R)
+  term2 <- log_diff_exp(term1,q_F+q_R) + l3 - l4
+  
+  log1m_exp(term2)
+}
+```
+
+$$
+\begin{aligned}
+P(macth | Obs(mismatch)) &= \frac{(1-e^{q_F})e^{q_R}}{4} + \frac{(1-e^{q_R})e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
+&= \frac{(1-e^{q_F})e^{q_R} + (1-e^{q_R})e^{q_F} + e^{q_F+q_R}}{4} \\
+&= \frac{e^{q_R} - e^{q_F+q_R} + e^{q_F} - e^{q_F+q_R} + e^{q_F+q_R}}{4} \\
+&= \frac{e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4}
+\end{aligned}
+$$
+
+```{r}
+Pm_mismatch_observed <- function(Q_F, Q_R) {
+  l10 <- log(10)
+  l3 <- log(3)
+  l4 <- log(4)
+
+  q_F <- -Q_F/10*l10
+  q_R <- -Q_R/10*l10
+  
+  term1 <- log_sum_exp(q_F,q_R)
+  log_diff_exp(term1,q_F+q_R) - l4
+}
+```
+
+```{r}
+score_match_observed <- function(Q_F, Q_R) {
+  Pm_match_observed(Q_F,Q_R) - log1m_exp(Pm_match_observed(Q_F,Q_R)) 
+}
+
+score_mismatch_observed <- function(Q_F, Q_R) {
+   Pm_mismatch_observed(Q_F,Q_R) - log1m_exp(Pm_mismatch_observed(Q_F,Q_R)) 
+}
+```
+
+```{r}
+scores <- expand_grid(QF=0:40,QR=0:40) %>%
+  mutate(score_match_observed = round(score_match_observed(QF,QR),2),
+         score_mismatch_observed = round(score_mismatch_observed(QF,QR),2))
+```
+
+```{r}
+plot_match <- plot_ly(scores, 
+        x=~QF, y=~QR, z=~score_match_observed, 
+        type="mesh3d") %>%
+    layout(
+        plot_bgcolor = "#bababa",
+        scene = list(
+            xaxis = list(title = "Q forward read"),   # Change x/y/z axis title
+            yaxis = list(title = "Q reverse read"),
+            zaxis = list(title = "Score match")))
+```
+
+```{r}
+plot_mismatch <- plot_ly(scores, 
+        x=~QF, y=~QR, z=~score_mismatch_observed, 
+        type="mesh3d") %>%
+    layout(
+        plot_bgcolor = "#bababa",
+        scene = list(
+            xaxis = list(title = "Q forward read"),   # Change x/y/z axis title
+            yaxis = list(title = "Q reverse read"),
+            zaxis = list(title = "Score mismatch")))
+```
+
+```{r}
+write(plotly_json(plot_match,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/match.json")
+write(plotly_json(plot_mismatch,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/mismatch.json")
+
+```
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/fasta_dotplot.png
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/fasta_dotplot.png
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/index.html
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+    <link>http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/</link>
+    <description>Recent content in The FASTA-like alignment on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/index.xml" rel="self" type="application/rss+xml" />
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+    <title>The OBITools4 commands on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/</link>
+    <description>Recent content in The OBITools4 commands on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
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+      <pubDate>Fri, 04 Oct 2024 17:16:03 +0200</pubDate>
+      <guid>http://metabar:8888/obidoc/docs/commands/tags/</guid>
+      <description>&lt;h1 id=&#34;glossary-of-tags&#34;&gt;&#xA;  Glossary of tags&#xA;  &lt;a class=&#34;anchor&#34; href=&#34;#glossary-of-tags&#34;&gt;#&lt;/a&gt;&#xA;&lt;/h1&gt;&#xA;&lt;h3 id=&#34;--d--&#34;&gt;&#xA;  - D -&#xA;  &lt;a class=&#34;anchor&#34; href=&#34;#--d--&#34;&gt;#&lt;/a&gt;&#xA;&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;definition&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;text information about the sequence present in the original sequence file.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;direction&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;set to “forward” if the original sequence did not need to be reverse-complemented to be processed, set to “reverse” otherwise.&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h3 id=&#34;--f--&#34;&gt;&#xA;  - F -&#xA;  &lt;a class=&#34;anchor&#34; href=&#34;#--f--&#34;&gt;#&lt;/a&gt;&#xA;&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;forward_error&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Number of mismatch between forward primer and priming site&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;forward_match&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Forward primer priming site sequence&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;forward_primer&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Forward primer sequence&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;</description>
+    </item>
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/options/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/options/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/options/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/options/index.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Shared command options on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/options/</link>
+    <description>Recent content in Shared command options on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/options/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/options/two_sequences.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/options/two_sequences.fasta
@@ -0,0 +1,6 @@
+>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
+ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
+agcttaaaactcaaaggacttggcggtgctttatatccct
+>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
+ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
+agcttaaaactcaaaggacctggcagttctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/commands/others/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/others/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/others/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/others/index.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Others on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/others/</link>
+    <description>Recent content in Others on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/others/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/tags/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/tags/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Taxonomy on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/taxonomy/</link>
+    <description>Recent content in Taxonomy on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/taxonomy/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/ecoPCRFormat
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/ecoPCRFormat
@@ -0,0 +1,604 @@
+#!/usr/bin/env python3
+
+import re
+import gzip
+import struct
+import sys
+import time
+import getopt
+from functools import cmp_to_key
+
+_dbenable=False
+
+#####
+#
+#
+# Generic file function
+#
+#
+#####
+
+def universalOpen(file):
+    if isinstance(file,str):
+        if file[-3:] == '.gz':
+            rep = gzip.open(file)
+        else:
+            rep = open(file)
+    else:
+        rep = file
+    return rep
+
+def universalTell(file):
+    if isinstance(file, gzip.GzipFile):
+        file=file.myfileobj
+    return file.tell()
+
+def fileSize(file):
+    if isinstance(file, gzip.GzipFile):
+        file=file.myfileobj
+    pos = file.tell()
+    file.seek(0,2)
+    length = file.tell()
+    file.seek(pos,0)
+    return length
+
+def progressBar(pos,max,reset=False,delta=[]):
+    if reset:
+        del delta[:]
+    if not delta:
+        delta.append(time.time())
+        delta.append(time.time())
+
+    delta[1]=time.time()
+    elapsed = delta[1]-delta[0]
+    percent = float(pos)/max * 100
+    remain = time.strftime('%H:%M:%S',time.gmtime(elapsed / percent * (100-percent)))
+    bar = '#' * int(percent/2)
+    bar+= '|/-\\-'[pos % 5]
+    bar+= ' ' * (50 - int(percent/2))
+    sys.stderr.write('\r%5.1f %% |%s] remain : %s' %(percent,bar,remain))
+
+#####
+#
+#
+# NCBI Dump Taxonomy reader
+#
+#
+#####
+
+def endLessIterator(endedlist):
+    for x in endedlist:
+        yield x
+    while(1):
+        yield endedlist[-1]
+   
+class ColumnFile(object):
+    
+    def __init__(self,stream,sep=None,strip=True,types=None):
+        if isinstance(stream,str):
+            self._stream = open(stream)
+        else:
+            try: 
+                iter(stream)
+                self._stream = stream
+            except TypeError:    
+                raise ValueError('stream must be string or an iterator')
+        self._delimiter=sep
+        self._strip=strip
+        if types:
+            self._types=[x for x in types]
+            for i in range(len(self._types)):
+                if self._types[i] is bool:
+                    self._types[i]=ColumnFile.str2bool
+        else:
+            self._types=None
+            
+    def str2bool(x):
+        return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False}))
+                    
+    str2bool = staticmethod(str2bool)
+            
+        
+    def __iter__(self):
+        return self
+    
+    def __next__(self):
+        ligne = next(self._stream)
+        data = ligne.split(self._delimiter)
+        if self._strip or self._types:
+            data = [x.strip() for x in data]
+        if self._types:
+            it = endLessIterator(self._types)
+            data = [x[1](x[0]) for x in ((y,next(it)) for y in data)]
+        return data
+    
+def taxonCmp(t1,t2):
+    if t1[0] < t2[0]:
+        return -1
+    elif t1[0] > t2[0]:
+        return +1
+    return 0
+
+def bsearchTaxon(taxonomy,taxid):
+    taxCount = len(taxonomy)
+    begin = 0
+    end   = taxCount 
+    oldcheck=taxCount
+    check = int(begin + end / 2)
+    while check != oldcheck and taxonomy[check][0]!=taxid :
+        if taxonomy[check][0] < taxid:
+            begin=check
+        else:
+            end=check
+        oldcheck=check
+        check = int((begin + end) / 2)
+        
+        
+    if taxonomy[check][0]==taxid:
+        return check
+    else:
+        return None
+        
+    
+    
+def readNodeTable(file):
+
+    file = universalOpen(file)
+    
+    nodes = ColumnFile(file, 
+                       sep='|', 
+                       types=(int,int,str,
+                              str,str,bool,
+                              int,bool,int,
+                              bool,bool,bool,str))
+    print("Reading taxonomy dump file...", file=sys.stderr)
+    taxonomy=[[n[0],n[2],n[1]] for n in nodes]
+    print("List all taxonomy rank...", file=sys.stderr)    
+    ranks =list(set(x[1] for x in taxonomy))
+    ranks.sort()
+    ranks = {rank: index for index, rank in enumerate(ranks)}
+    
+    print("Sorting taxons...", file=sys.stderr)
+    taxonomy.sort(key=lambda x: x[0])
+
+    print("Indexing taxonomy...", file=sys.stderr)
+    index = {}
+    for t in taxonomy:
+        index[t[0]]=bsearchTaxon(taxonomy, t[0])
+    
+    print("Indexing parent and rank...", file=sys.stderr)
+    for t in taxonomy:
+        t[1]=ranks[t[1]]
+        t[2]=index[t[2]]
+        
+        
+    return taxonomy,ranks,index
+
+def nameIterator(file):
+    file = universalOpen(file)
+    names = ColumnFile(file, 
+                       sep='|', 
+                       types=(int,str,
+                              str,str))
+    for taxid,name,unique,classname,white in names:
+        yield taxid,name,classname
+        
+def mergedNodeIterator(file):
+    file = universalOpen(file)
+    merged = ColumnFile(file, 
+                       sep='|', 
+                       types=(int,int,str))
+    for taxid,current,white in merged:
+            yield taxid,current
+    
+def deletedNodeIterator(file):
+    file = universalOpen(file)
+    deleted = ColumnFile(file, 
+                       sep='|', 
+                       types=(int,str))
+    for taxid,white in deleted:
+            yield taxid
+    
+def readTaxonomyDump(taxdir):
+    taxonomy,ranks,index = readNodeTable('%s/nodes.dmp' % taxdir)
+    
+    print("Adding scientific name...", file=sys.stderr)
+
+    alternativeName=[]
+    for taxid,name,classname in nameIterator('%s/names.dmp' % taxdir):
+        alternativeName.append((name,classname,index[taxid]))
+        if classname == 'scientific name':
+            taxonomy[index[taxid]].append(name)
+        
+    print("Adding taxid alias...", file=sys.stderr)
+    for taxid,current in mergedNodeIterator('%s/merged.dmp' % taxdir):
+        index[taxid]=index[current]
+    
+    print("Adding deleted taxid...", file=sys.stderr)
+    for taxid in deletedNodeIterator('%s/delnodes.dmp' % taxdir):
+        index[taxid]=None
+    
+    return taxonomy,ranks,alternativeName,index
+
+#####
+#
+#
+#  Genbank/EMBL sequence reader
+#
+#
+#####
+
+def entryIterator(file):
+    file = universalOpen(file)
+    rep =[]
+    ligne = file.readline()
+    while ligne:
+        rep.append(ligne)
+        if ligne == '//\n':
+            rep = ''.join(rep)
+            yield rep
+            rep = []
+        ligne = file.readline()
+            
+def fastaEntryIterator(file):
+    file = universalOpen(file)
+    rep =[]
+    ligne =  file.readline()
+    while ligne:
+        if ligne[0] == '>' and rep:
+            rep = ''.join(rep)
+            yield rep
+            rep = []
+        rep.append(ligne)
+        ligne = file.readline()
+
+    if rep:
+        rep = ''.join(rep)
+        yield rep
+    
+_cleanSeq = re.compile('[ \n0-9]+')
+            
+def cleanSeq(seq):
+    return _cleanSeq.sub('',seq)
+    
+    
+_gbParseID = re.compile('(?<=^LOCUS {7})[^ ]+(?= )',re.MULTILINE)   
+_gbParseDE = re.compile('(?<=^DEFINITION {2}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)   
+_gbParseSQ = re.compile('(?<=^ORIGIN).+?(?=^//$)',re.MULTILINE+re.DOTALL)  
+_gbParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
+  
+def genbankEntryParser(entry):
+    Id = _gbParseID.findall(entry)[0]
+    De = ' '.join(_gbParseDE.findall(entry)[0].split())
+    Sq = cleanSeq(_gbParseSQ.findall(entry)[0].upper())
+    try:
+        Tx = int(_gbParseTX.findall(entry)[0])
+    except IndexError:
+        Tx = None
+    return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
+
+######################
+
+_cleanDef = re.compile('[\nDE]')
+
+def cleanDef(definition):
+    return _cleanDef.sub('',definition)
+
+_emblParseID = re.compile('(?<=^ID {3})[^ ]+(?=;)',re.MULTILINE)   
+_emblParseDE = re.compile('(?<=^DE {3}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)   
+_emblParseSQ = re.compile('(?<=^  ).+?(?=^//$)',re.MULTILINE+re.DOTALL)  
+_emblParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
+
+def emblEntryParser(entry):
+    Id = _emblParseID.findall(entry)[0]
+    De = ' '.join(cleanDef(_emblParseDE.findall(entry)[0]).split())
+    Sq = cleanSeq(_emblParseSQ.findall(entry)[0].upper())
+    try:
+        Tx = int(_emblParseTX.findall(entry)[0])
+    except IndexError:
+        Tx = None
+    return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
+
+
+######################
+
+_fastaSplit=re.compile(';\\W*')
+
+def parseFasta(seq):
+    seq=seq.split('\n')
+    title = seq[0].strip()[1:].split(None,1)
+    id=title[0]
+    if len(title) == 2:
+        field = _fastaSplit.split(title[1])
+    else:
+        field=[]
+    info = dict(x.split('=',1) for x in field if '=' in x)
+    definition = ' '.join([x for x in field if '=' not in x])
+    seq=(''.join([x.strip() for x in seq[1:]])).upper()   
+    return id,seq,definition,info
+
+  
+def fastaEntryParser(entry):
+    id,seq,definition,info = parseFasta(entry)
+    Tx = info.get('taxid',None)   
+    if Tx is not None:
+        match = re.search(r'taxon:(\d+)', Tx)
+        if match:
+            Tx = match.group(1)
+        Tx=int(Tx)
+    return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}
+    
+
+def sequenceIteratorFactory(entryParser,entryIterator):
+    def sequenceIterator(file):
+        for entry in entryIterator(file):
+            yield entryParser(entry)
+    return sequenceIterator
+
+
+def taxonomyInfo(entry,connection):
+    taxid = entry['taxid']
+    curseur = connection.cursor()
+    curseur.execute("""
+                        select taxid,species,genus,family,
+                               taxonomy.scientificName(taxid) as sn,
+                               taxonomy.scientificName(species) as species_sn,
+                               taxonomy.scientificName(genus) as genus_sn,
+                               taxonomy.scientificName(family) as family_sn
+                        from
+                            (   
+                             select alias                      as taxid,
+                               taxonomy.getSpecies(alias) as species,
+                               taxonomy.getGenus(alias)   as genus,
+                               taxonomy.getFamily(alias)  as family
+                                from taxonomy.aliases
+                               where id=%d ) as tax
+                    """ % taxid)
+    rep = curseur.fetchone()
+    entry['current_taxid']=rep[0]
+    entry['species']=rep[1]
+    entry['genus']=rep[2]
+    entry['family']=rep[3]
+    entry['scientific_name']=rep[4]
+    entry['species_sn']=rep[5]
+    entry['genus_sn']=rep[6]
+    entry['family_sn']=rep[7]
+    return entry
+    
+#####
+#
+#
+# Binary writer
+#
+#
+#####
+    
+def ecoSeqPacker(sq):
+    
+    compactseq = gzip.zlib.compress(bytes(sq['sequence'],"ascii"),9)
+    cptseqlength  = len(compactseq)
+    delength   = len(sq['definition'])
+    
+    totalSize = 4 + 20 + 4 + 4 + 4 + cptseqlength + delength
+    
+    packed = struct.pack('> I I 20s I I I %ds %ds' % (delength,cptseqlength),
+                         totalSize,
+                         sq['taxid'],
+                         bytes(sq['id'],"ascii"),
+                         delength,
+                         len(sq['sequence']),
+                         cptseqlength,
+                         bytes(sq['definition'],"ascii"),
+                         compactseq)
+    
+    assert len(packed) == totalSize+4, "error in sequence packing"
+    
+    return packed
+
+def ecoTaxPacker(tx):
+    
+    namelength = len(tx[3])
+    
+    totalSize = 4 + 4 + 4 + 4 + namelength
+    
+    packed = struct.pack('> I I I I I %ds' % namelength, 
+                         totalSize, 
+                         tx[0],
+                         tx[1],
+                         tx[2], 
+                         namelength,
+                         bytes(tx[3],"ascii"))
+    
+    return packed
+
+def ecoRankPacker(rank):
+    
+    namelength = len(rank)
+    
+    packed = struct.pack('> I %ds' % namelength,
+                         namelength,
+                         bytes(rank, 'ascii'))
+    
+    return packed
+                
+def ecoNamePacker(name):
+    
+    namelength = len(name[0])
+    classlength= len(name[1])
+    totalSize =  namelength + classlength + 4 + 4 + 4 + 4
+    
+    packed = struct.pack('> I I I I I %ds %ds' % (namelength,classlength),
+                         totalSize,
+                         int(name[1]=='scientific name'),
+                         namelength,
+                         classlength,
+                         name[2],
+                         bytes(name[0], 'ascii'),
+                         bytes(name[1], 'ascii'))
+    
+    return packed
+    
+def ecoSeqWriter(file,input,taxindex,parser):
+    output = open(file,'wb')
+    input  = universalOpen(input)
+    inputsize = fileSize(input)
+    entries = parser(input)
+    seqcount=0
+    skipped = []
+
+    output.write(struct.pack('> I',seqcount))
+    
+    progressBar(1, inputsize,reset=True)
+    for entry in entries:
+        if entry['taxid'] is not None:
+            try:
+                entry['taxid']=taxindex[entry['taxid']]
+            except KeyError:
+                entry['taxid']=None
+            if entry['taxid'] is not None:
+                seqcount+=1
+                output.write(ecoSeqPacker(entry))
+            else:
+                skipped.append(entry['id'])
+            where = universalTell(input)
+            progressBar(where, inputsize)
+            print(" Readed sequences : %d     " % seqcount, end=' ', file=sys.stderr)
+        else:
+            skipped.append(entry['id'])
+        
+    print(file=sys.stderr)
+    output.seek(0,0)
+    output.write(struct.pack('> I',seqcount))
+    
+    output.close()
+    return skipped
+        
+
+def ecoTaxWriter(file,taxonomy):
+    output = open(file,'wb')
+    output.write(struct.pack('> I',len(taxonomy)))
+    
+    for tx in taxonomy:
+        output.write(ecoTaxPacker(tx))
+
+    output.close()
+    
+def ecoRankWriter(file,ranks):
+    output = open(file,'wb')
+    output.write(struct.pack('> I',len(ranks)))
+
+    rankNames = list(ranks.keys())
+    rankNames.sort()
+    
+    for rank in rankNames:
+        output.write(ecoRankPacker(rank))
+
+    output.close()
+
+def nameCmp(n1,n2):
+    name1=n1[0].upper()
+    name2=n2[0].upper()
+    if name1 < name2:
+        return -1
+    elif name1 > name2:
+        return 1
+    return 0
+
+
+def ecoNameWriter(file,names):
+    output = open(file,'wb')
+    output.write(struct.pack('> I',len(names)))
+
+    names.sort(key=lambda x:x[0].upper())
+    
+    for name in names:
+        output.write(ecoNamePacker(name))
+
+    output.close()
+    
+def ecoDBWriter(prefix,taxonomy,seqFileNames,parser):
+    
+    ecoRankWriter('%s.rdx' % prefix, taxonomy[1])
+    ecoTaxWriter('%s.tdx' % prefix, taxonomy[0])
+    ecoNameWriter('%s.ndx' % prefix, taxonomy[2])
+  
+    filecount = 0
+    for filename in seqFileNames:
+        filecount+=1
+        sk=ecoSeqWriter('%s_%03d.sdx' % (prefix,filecount), 
+                     filename, 
+                     taxonomy[3], 
+                     parser)
+        if sk:
+            print("Skipped entry :", file=sys.stderr)
+            print(sk, file=sys.stderr)
+        
+def ecoParseOptions(arguments):
+    opt = {
+            'prefix' : 'ecodb',
+            'taxdir' : 'taxdump',
+            'parser' : sequenceIteratorFactory(genbankEntryParser,
+                                                  entryIterator)
+           }
+    
+    o,filenames = getopt.getopt(arguments,
+                                'ht:T:n:gfe',
+                                ['help',
+                                 'taxonomy=',
+                                 'taxonomy_db=',
+                                 'name=',
+                                 'genbank',
+                                 'fasta',
+                                 'embl'])
+    
+    for name,value in o:
+        if name in ('-h','--help'):
+            printHelp()
+            exit()
+        elif name in ('-t','--taxonomy'):
+            opt['taxmod']='dump'
+            opt['taxdir']=value
+        elif name in ('-T','--taxonomy_db'):
+            opt['taxmod']='db'
+            opt['taxdb']=value
+        elif name in ('-n','--name'):
+            opt['prefix']=value
+        elif name in ('-g','--genbank'):
+            opt['parser']=sequenceIteratorFactory(genbankEntryParser,
+                                                  entryIterator)
+
+        elif name in ('-f','--fasta'):
+            opt['parser']=sequenceIteratorFactory(fastaEntryParser,
+                                                  fastaEntryIterator)
+            
+        elif name in ('-e','--embl'):
+            opt['parser']=sequenceIteratorFactory(emblEntryParser,
+                                                  entryIterator)
+        else:
+            raise ValueError('Unknown option %s' % name)
+
+    return opt,filenames
+
+def printHelp():
+    print("-----------------------------------")
+    print(" ecoPCRFormat.py")
+    print("-----------------------------------")
+    print("ecoPCRFormat.py [option] <argument>")
+    print("-----------------------------------")
+    print("-e    --embl        :[E]mbl format")
+    print("-f    --fasta       :[F]asta format")
+    print("-g    --genbank     :[G]enbank format")
+    print("-h    --help        :[H]elp - print this help")
+    print("-n    --name        :[N]ame of the new database created")
+    print("-t    --taxonomy    :[T]axonomy - path to the taxonomy database")
+    print("                    :bcp-like dump from GenBank taxonomy database.")
+    print("-----------------------------------")
+
+if __name__ == '__main__':
+    
+    opt,filenames = ecoParseOptions(sys.argv[1:])
+    
+    taxonomy = readTaxonomyDump(opt['taxdir'])
+    
+    ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])
+    
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Designing new barcodes on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/cookbook/ecoprimers/</link>
+    <description>Recent content in Designing new barcodes on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/ecoprimers/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/ncbi-ftp.png
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/ncbi-ftp.png
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
@@ -0,0 +1,103 @@
+SHELL := /bin/bash
+FTPNCBI=ftp.ncbi.nlm.nih.gov
+GBURL=https://$(FTPNCBI)/genbank
+GBRELEASE_URL=$(GBURL)/GB_Release_Number
+
+TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
+
+GBRELEASE:=$(shell curl $(GBRELEASE_URL))
+
+GBDIV_ALL:=$(shell curl -L ${GBURL} \
+                  | grep -E 'gb.+\.seq\.gz' \
+				  | sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
+				  | sort \
+				  | uniq)
+
+GBDIV=bct inv mam phg pln pri rod vrl vrt
+DIRECTORIES=fasta fasta_fgs
+
+GBFILE_ALL:=$(shell curl -L ${GBURL} \
+					| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
+					| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
+
+
+SUFFIXES += .d
+NODEPS:=clean taxonomy
+DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
+
+ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
+    #Chances are, these files don't exist.  GMake will create them and
+    #clean up automatically afterwards
+    -include $(DEPFILES)
+endif
+
+
+all: depends directories FORCE
+	@make downloads
+
+downloads: taxonomy fasta_files 
+	@echo Genbank Release number $(GBRELEASE)
+	@echo all divisions : $(GBDIV_ALL)
+
+FORCE:
+	@sleep 1
+
+.PHONY: all directories depends taxonomy fasta_files FORCE
+
+depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
+
+division: $(GBDIV)
+
+taxonomy: directories Release_$(GBRELEASE)/taxonomy
+
+directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp 
+
+Release_$(GBRELEASE):
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
+	@echo Create depends directory
+	@mkdir -p Release_$(GBRELEASE)/depends
+	@for f in ${GBFILE_ALL} ; do \
+	            echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
+				echo -e "\t@echo Downloading file : $$f..." ; \
+				echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
+				echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
+				echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@"  ; \
+				echo ; \
+				div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
+				fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
+				fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
+				fasta_files="$$fasta_files $$fasta" ; \
+				fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
+				echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
+				echo -e "\t@echo converting file : \$$< in fasta" ; \
+				echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
+				echo -e "\t@obiconvert -Z --fasta-output --skip-empty  \\" ; \
+				echo -e "\t            Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
+				echo -e "\t            && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@  \\" ; \
+				echo -e "\t            && rm -f Release_$(GBRELEASE)/tmp/$$f  \\" ; \
+				echo -e "\t            || rm -f \$$@" ; \
+				echo -e "\t@echo conversion of $$@ done." ; \
+				echo ; \
+				done > $@ ; \
+				echo >> $@ ; \
+				echo "fasta_files: $$fasta_files" >> $@ ; 
+
+Release_$(GBRELEASE)/taxonomy: 
+	mkdir -p $@
+	curl -iL $(TAXOURL) \
+	| tar -C $@ -zxf -  
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Analysing an Illumina data set on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/cookbook/illumina/</link>
+    <description>Recent content in Analysing an Illumina data set on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/illumina/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/length-plot.png
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/length-plot.png
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/ncbitaxo.tgz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/ncbitaxo.tgz
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/unidentified.fastq
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/unidentified.fastq
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf.fastq
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf.fastq
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled.fastq
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled.fastq
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_1_percent.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_1_percent.fasta
@@ -0,0 +1,26 @@
+>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
+gcctgaaactcaaaggacttggcggtgctttacatccct
+>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
+ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
+ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
+>HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
+tttt
+>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
+ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
+gattaaacctcaaaggacttggcagtgctttatacccct
+>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned.fastq
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned.fastq
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_simple.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_simple.fasta
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_simple_clean.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_simple_clean.fasta
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_uniq.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_uniq.fasta
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_no_short.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_no_short.fasta
@@ -0,0 +1,24 @@
+>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
+gcctgaaactcaaaggacttggcggtgctttacatccct
+>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
+ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
+ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
+>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
+ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
+gattaaacctcaaaggacttggcagtgctttatacccct
+>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_no_singleton.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_no_singleton.fasta
@@ -0,0 +1,329 @@
+>HELIUM_000100422_612GNAAXX:7:56:19300:10949#0/1_sub[28..127] {"count":37,"merged_sample":{"29a_F260619":37},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":43}}
+ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactagcggcaac
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--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_taxo.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_taxo.fasta
@@ -0,0 +1,24 @@
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--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final.fasta
@@ -0,0 +1,24 @@
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+ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
+>seq0005 {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","seq_number":5,"taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
+ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
+gattaaacctcaaaggacttggcagtgctttatacccct
+>seq0006 {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":6,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>seq0007 {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":7,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>seq0008 {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":8,"taxid":"taxon:9611 [Canis]@genus"}
+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_motus.csv
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_motus.csv
@@ -0,0 +1,9 @@
+id,count,obitag_bestid,obitag_bestmatch,obitag_match_count,obitag_rank,obitag_similarity_method,seq_number,taxid,sequence
+seq0001,10172,0.9797979797979798,AY227529,1,genus,lcs,1,taxon:9992 [Marmota]@genus,ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
+seq0002,260,0.9405940594059405,AF154263,9,infraorder,lcs,2,taxon:35500 [Pecora]@infraorder,ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaacagcttaaaactcaaaggacttggcggtgctttataccctt
+seq0003,7146,1,AB245427,1,species,lcs,3,taxon:9860 [Cervus elaphus]@species,ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
+seq0004,87,0.9494949494949495,AY227530,2,tribe,lcs,4,taxon:337730 [Marmotini]@tribe,ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
+seq0005,95,0.9595959595959596,AC187326,1,subspecies,lcs,5,taxon:9615 [Canis lupus familiaris]@subspecies,ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaacagattaaacctcaaaggacttggcagtgctttatacccct
+seq0006,12004,1,AJ885202,1,species,lcs,6,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
+seq0007,319,1,AJ972683,1,species,lcs,7,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
+seq0008,366,1,AB048590,1,genus,lcs,8,taxon:9611 [Canis]@genus,ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_occurrency.csv
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_occurrency.csv
@@ -0,0 +1,6 @@
+id,seq0001,seq0002,seq0003,seq0004,seq0005,seq0006,seq0007,seq0008
+29a_F260619,0,337,0,0,105,5789,376,1
+15a_F730814,0,0,0,0,0,8822,0,5
+13a_F730603,0,0,8039,0,0,0,0,17
+26a_F040644,12205,0,0,202,12,0,0,468
+
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_minimal.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_minimal.fasta
@@ -0,0 +1,24 @@
+>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
+gcctgaaactcaaaggacttggcggtgctttacatccct
+>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
+ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
+ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
+>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
+ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
+gattaaacctcaaaggacttggcagtgctttatacccct
+>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/variants-plot.png
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/variants-plot.png
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/db_v05_r117.fasta.gz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/db_v05_r117.fasta.gz
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_F.fastq.gz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_F.fastq.gz
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_R.fastq.gz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_R.fastq.gz
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_diet_ngsfilter.csv
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_diet_ngsfilter.csv
@@ -0,0 +1,8 @@
+@param,matching,strict
+@param,primer_mismatches,2
+@param,indels,false
+experiment,sample,sample_tag,forward_primer,reverse_primer
+wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_diet_dataset.tgz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_diet_dataset.tgz
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/index.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Cookbook on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/cookbook/</link>
+    <description>Recent content in Cookbook on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/Makefile
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/Makefile
@@ -0,0 +1,102 @@
+SHELL := /bin/bash
+FTPNCBI=ftp.ncbi.nlm.nih.gov
+GBURL=https://$(FTPNCBI)/genbank
+GBRELEASE_URL=$(GBURL)/GB_Release_Number
+
+TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
+
+GBRELEASE:=$(shell curl $(GBRELEASE_URL))
+
+GBDIV_ALL:=$(shell curl -L ${GBURL} \
+                  | grep -E 'gb.+\.seq\.gz' \
+				  | sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
+				  | sort \
+				  | uniq)
+
+GBDIV=bct inv mam phg pln pri rod vrl vrt
+DIRECTORIES=fasta fasta_fgs
+
+GBFILE_ALL:=$(shell curl -L ${GBURL} \
+					| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
+					| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
+
+
+SUFFIXES += .d
+NODEPS:=clean taxonomy
+DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
+
+ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
+    #Chances are, these files don't exist.  GMake will create them and
+    #clean up automatically afterwards
+    -include $(DEPFILES)
+endif
+
+
+all: depends directories FORCE
+	@make downloads
+
+downloads: taxonomy fasta_files 
+	@echo Genbank Release number $(GBRELEASE)
+	@echo all divisions : $(GBDIV_ALL)
+
+FORCE:
+
+.PHONY: all directories depends taxonomy fasta_files FORCE
+
+depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
+
+division: $(GBDIV)
+
+taxonomy: directories Release_$(GBRELEASE)/taxonomy
+
+directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp 
+
+Release_$(GBRELEASE):
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
+	@mkdir -p $@ 
+	@echo Create $@ directory
+
+Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
+	@echo Create depends directory
+	@mkdir -p Release_$(GBRELEASE)/depends
+	@for f in ${GBFILE_ALL} ; do \
+	            echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
+				echo -e "\t@echo Downloading file : $$f..." ; \
+				echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
+				echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
+				echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@"  ; \
+				echo ; \
+				div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
+				fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
+				fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
+				fasta_files="$$fasta_files $$fasta" ; \
+				fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
+				echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
+				echo -e "\t@echo converting file : \$$< in fasta" ; \
+				echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
+				echo -e "\t@obiconvert -Z --fasta-output --skip-empty  \\" ; \
+				echo -e "\t            Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
+				echo -e "\t            && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@  \\" ; \
+				echo -e "\t            && rm -f Release_$(GBRELEASE)/tmp/$$f  \\" ; \
+				echo -e "\t            || rm -f \$$@" ; \
+				echo -e "\t@echo conversion of $$@ done." ; \
+				echo ; \
+				done > $@ ; \
+				echo >> $@ ; \
+				echo "fasta_files: $$fasta_files" >> $@ ; 
+
+Release_$(GBRELEASE)/taxonomy: 
+	mkdir -p $@
+	curl -iL $(TAXOURL) \
+	| tar -C $@ -zxf -  
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Prepare a local copy of Genbank on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/cookbook/local_genbank/</link>
+    <description>Recent content in Prepare a local copy of Genbank on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/local_genbank/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Oxford Nanopore data analysis on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/cookbook/minion/</link>
+    <description>Recent content in Oxford Nanopore data analysis on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/minion/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Build a reference database on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/cookbook/reference_db/</link>
+    <description>Recent content in Build a reference database on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/reference_db/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/index.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>File formats on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/file_format/</link>
+    <description>Recent content in File formats on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <atom:link href="http://metabar:8888/obidoc/docs/file_format/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/annotations/index.html
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+>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
+ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
+agcttaaaactcaaaggacttggcggtgctttatatccct
+>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
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+agcttaaaactcaaaggacctggcagttctttatatccct
--- a/Show More
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				`@@ -0,0 +1 @@`
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				`@@ -0,0 +1 @@`
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