doc/sphinx/source/attributes.rst

@@ -9,6 +9,8 @@ Contents:
 .. toctree::
    :maxdepth: 2
    
+   attributes/avg_quality 
+   attributes/complemented 
    attributes/count 
    attributes/cut 
    attributes/direction 
@@ -19,10 +21,14 @@ Contents:
    attributes/forward_error 
    attributes/forward_match 
    attributes/forward_primer 
+   attributes/forward_score 
    attributes/forward_tag 
    attributes/forward_tm 
    attributes/genus 
    attributes/genus_name 
+   attributes/head_quality 
+   attributes/merged_star 
+   attributes/mid_quality 
    attributes/mode 
    attributes/occurrence 
    attributes/order 
@@ -33,16 +39,19 @@ Contents:
    attributes/reverse_error 
    attributes/reverse_match 
    attributes/reverse_primer 
+   attributes/reverse_score 
    attributes/reverse_tag 
    attributes/reverse_tm 
    attributes/sample 
    attributes/scientific_name 
    attributes/score 
    attributes/seq_length 
+   attributes/seq_length_ori
    attributes/sminL 
    attributes/sminR 
    attributes/species 
    attributes/species_name 
    attributes/status 
+   attributes/tail_quality
    attributes/taxid
    

doc/sphinx/source/attributes/merged_star.rst

@@ -2,11 +2,11 @@ merged_*
 ========
 
     The `merged_*` attribute is built based on another attribute `*` (for example, 
-    `sample`). `merged_*` is a dictionary with the values of the `*` attribute as 
-    keys, and the numbers of times the sequence was observed for each key as 
-    corresponding values. For instance, `merged_sample={'X1':12, 'X2'=10}` 
-    means that the sequence was observed 12 times in the sample 'X1' and 10 times 
-    in the sample 'X2'.
+    `sample`) by the :doc:`obiuniq <../scripts/obiuniq>` program. The value associated to the `merged_*` 
+    attribute is a contingency table summarizing modality frequencies associated to the `*` attribute.
+    For instance, `merged_sample={'X1':12, 'X2':10}` means that among the 22 identical sequences merged 
+    by the :doc:`obiuniq <../scripts/obiuniq>`, the `sample` attribute was set 12 and 10 times to the modality 'X1' 
+    and 'X2', respectively.
     
     Attribute added by the program:
         - :doc:`obiuniq <../scripts/obiuniq>`

doc/sphinx/source/obitaxonomy.rst

@@ -1,3 +1,25 @@
 The OBITools formatted taxonomy
 ===============================
 
+Management of the taxonomy
+--------------------------
+
+Filtering and annotation steps in the processing of DNA metabarcoding sequence data are greatly 
+eased by the explicit association of taxonomic information to sequences together with an easy 
+access to the taxonomy. Taxonomic information, including a taxonomic identifier, can thus be 
+stored in the set of attributes of each sequence record. Specifically, the `taxid` attribute 
+is used by the OBITools when querying taxonomic information of a sequence record, nevertheless 
+several OBITools commands can annotate sequence records with taxonomy-related attributes for 
+the user's convenience. The value of the `taxid` attribute must be a unique integer referring 
+unambiguously to one taxon in the taxonomic associated database. Although this is not mandatory, 
+the NCBI taxonomy is a preferred source of taxonomic information as the OBITools provide commands 
+to easily extract the full taxonomic information from it. The command `obitaxonomy` is useful to 
+build a taxonomic database in the OBITools format from a dump of the NCBI taxonomic database 
+(downloadable at the following URL: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz). 
+Moreover, the `obitaxonomy` command can enrich an existing taxonomy with private taxa, therefore 
+enabling to associate sequence records to taxa not initially present in the reference taxonomic database. 
+As the OBITools have access to the full taxonomic tree topology, they are able to inform higher taxonomic 
+levels from a taxon identifier (e.g. the family, order, class, phylum, etc. corresponding to a genus) 
+leading to efficient and simple annotation and querying of taxonomic information. 
+
+