MetabarcodingSchool/OBIJupyterHub
1
0
Fork 0
Code Issues Pull Requests 1 Actions Packages Projects Releases Wiki Activity

Make cleaning

Browse Source
This commit is contained in:
Eric Coissac
2025-11-16 14:56:03 +01:00
parent 35d275c104
commit 30b7175702
367 changed files with 170866 additions and 11173 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2143
jupyterhub_volumes/web/obidoc/obitools/obimultiplex/index.html Normal file
View File

File diff suppressed because it is too large Load Diff

12
jupyterhub_volumes/web/obidoc/obitools/obimultiplex/index.xml Normal file
View File

@@ -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>obimultiplex on OBITools4 documentation</title>
<link>http://metabar:8888/obidoc/obitools/obimultiplex/</link>
<description>Recent content in obimultiplex on OBITools4 documentation</description>
<generator>Hugo</generator>
<language>en-us</language>
<lastBuildDate></lastBuildDate>
<atom:link href="http://metabar:8888/obidoc/obitools/obimultiplex/index.xml" rel="self" type="application/rss+xml" />
</channel>
</rss>

5
jupyterhub_volumes/web/obidoc/obitools/obimultiplex/samples_extra.csv Normal file
View File

@@ -0,0 +1,5 @@
experiment,sample,sample_tag,forward_primer,reverse_primer,sex,age,plate,position
wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG,male,adult,02,A03
wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG,male,juvenile,02,A01
wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG,female,adult,01,B08
wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG,female,adult,01,B12
1 experiment sample sample_tag forward_primer reverse_primer sex age plate position
2 wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG male adult 02 A03
3 wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG male juvenile 02 A01
4 wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG female adult 01 B08
5 wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG female adult 01 B12

5
jupyterhub_volumes/web/obidoc/obitools/obimultiplex/samples_simple.csv Normal file
View File

@@ -0,0 +1,5 @@
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
1 experiment sample sample_tag forward_primer reverse_primer
2 wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG
3 wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG
4 wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG
5 wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG

16
jupyterhub_volumes/web/obidoc/obitools/obimultiplex/wolf_4seq.fastq Normal file
View File

@@ -0,0 +1,16 @@
@HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/1
ccaattaactagaacaggctcgtctagaagggtataaagcaccgccaagtcctttgagttttaagctattgccggtagtactctggcgaatagttttgtttgcataactatttgtgtttaaggctaggcatagtggggtatctaagttaattgg
+
CCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCC=CBCCBCBCCCCCCDEFAEDEEEEBEAEJEJ?D?CD@^aVca\C????CEBC>I?D<>EEDDDEEEEEEEAFEEDECCCCCCCCCCCCCCCBCCCCCCBCCCCCCCCCDCCCCCCCCCCCBC
@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/1
ccgaatatcttagataccccactatgcttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccctctagaggagcctgttctagatattcgg
+
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCacZXceafbd_e_bVb`cb[WZb]aaaaV`ECDDCEDCDKECFFEEEEEDEDEEJEEE@EEJECCCCCBCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCBCC
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
+
CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
@HELIUM_000100422_612GNAAXX:7:108:6440:4223#0/1
ccgcctcctttagatcccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
+
CCCCCCCBCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC

4
jupyterhub_volumes/web/obidoc/obitools/obimultiplex/wolf_4seq_bad.fastq Normal file
View File

@@ -0,0 +1,4 @@
@HELIUM_000100422_612GNAAXX:7:108:6440:4223#0/1 {"obimultiplex_error":"No barcode identified"}
ccgcctcctttagatcccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
+
CCCCCCCBCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC

12
jupyterhub_volumes/web/obidoc/obitools/obimultiplex/wolf_4seq_extra.fastq Normal file
View File

@@ -0,0 +1,12 @@
@HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/1_sub[28..127] {"age":"adult","experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"reverse","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"aattaac","obimultiplex_forward_tag":"aattaac","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":1,"obimultiplex_reverse_match":"tagaacaggctcgtctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"aattaac","obimultiplex_reverse_tag":"aattaac","obimultiplex_reverse_tag_dist":0,"plate":"02","position":"A03","sample":"13a_F730603","sex":"male"}
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
+
CCCBCCCCCCCCCCCCCCCEDEEFAEEEEEEEDDDEE><D?I>CBEC????C\acVa^@DC?D?JEJEAEBEEEEDEAFEDCCCCCCBCBCCBC=CCCCC
@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/1_sub[28..126] {"age":"adult","experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"forward","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"gaatatc","obimultiplex_forward_tag":"gaatatc","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":0,"obimultiplex_reverse_match":"tagaacaggctcctctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"gaatatc","obimultiplex_reverse_tag":"gaatatc","obimultiplex_reverse_tag_dist":0,"plate":"01","position":"B08","sample":"26a_F040644","sex":"female"}
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
+
CCCCCCCCCCCCCCCCCCacZXceafbd_e_bVb`cb[WZb]aaaaV`ECDDCEDCDKECFFEEEEEDEDEEJEEE@EEJECCCCCBCCCCCCCCCCCC
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1_sub[28..127] {"age":"adult","experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"forward","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"gcctcct","obimultiplex_forward_tag":"gcctcct","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":0,"obimultiplex_reverse_match":"tagaacaggctcctctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"gcctcct","obimultiplex_reverse_tag":"gcctcct","obimultiplex_reverse_tag_dist":0,"plate":"01","position":"B12","sample":"29a_F260619","sex":"female"}
ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
+
CCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCC

12
jupyterhub_volumes/web/obidoc/obitools/obimultiplex/wolf_4seq_simple.fastq Normal file
View File

@@ -0,0 +1,12 @@
@HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/1_sub[28..127] {"experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"reverse","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"aattaac","obimultiplex_forward_tag":"aattaac","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":1,"obimultiplex_reverse_match":"tagaacaggctcgtctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"aattaac","obimultiplex_reverse_tag":"aattaac","obimultiplex_reverse_tag_dist":0,"sample":"13a_F730603"}
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
+
CCCBCCCCCCCCCCCCCCCEDEEFAEEEEEEEDDDEE><D?I>CBEC????C\acVa^@DC?D?JEJEAEBEEEEDEAFEDCCCCCCBCBCCBC=CCCCC
@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/1_sub[28..126] {"experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"forward","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"gaatatc","obimultiplex_forward_tag":"gaatatc","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":0,"obimultiplex_reverse_match":"tagaacaggctcctctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"gaatatc","obimultiplex_reverse_tag":"gaatatc","obimultiplex_reverse_tag_dist":0,"sample":"26a_F040644"}
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
+
CCCCCCCCCCCCCCCCCCacZXceafbd_e_bVb`cb[WZb]aaaaV`ECDDCEDCDKECFFEEEEEDEDEEJEEE@EEJECCCCCBCCCCCCCCCCCC
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1_sub[28..127] {"experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"forward","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"gcctcct","obimultiplex_forward_tag":"gcctcct","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":0,"obimultiplex_reverse_match":"tagaacaggctcctctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"gcctcct","obimultiplex_reverse_tag":"gcctcct","obimultiplex_reverse_tag_dist":0,"sample":"29a_F260619"}
ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
+
CCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCC