--no commit message

doc/sphinx/source/wolves.rst

@@ -17,13 +17,13 @@ How to analyze DNA metabarcoding data produced on Illumina sequencers using:
 | use :                                                       |
 |                                                             |
 | - :doc:`obicount <scripts/obicount>` to count for the number|
-| of sequence records in a file                               |
+|   of sequence records in a file                             |
 | - :doc:`obihead <scripts/obihead>` and                      | 
-| :doc:`obitail <scripts/obitail>` to view the first          |
-| or last sequence records of a file                          |
-| - :doc:`obistatobistat` to get some basic statistics (count,|
-|   mean, standard deviation) on the attributes               |
-|   (key=value couples) in the fasta header of each           |
+|   :doc:`obitail <scripts/obitail>` to view the first        |
+|   or last sequence records of a file                        |
+| - :doc:`obistat <scripts/obistat>` to get some basic        |
+|   statistics (count, mean, standard deviation) on the       |
+|   attributes (key=value couples) in the fasta header of each|
 |   sequence record (see The `extended OBITools fasta format` |
 |   in the :doc:`fasta format <fasta>` description)           |
 | - any *Unix* command such as ``less``, ``awk``, ``sort``,   |
@@ -47,12 +47,12 @@ The data needed to run the tutorial are the following:
 - the file describing the primers and tags used for all samples sequenced:
 
     * ``wolf_ngsfilter.txt``
-    The tags correspond to short and specific sequences added on the 5' end of each primer to distinguish the different samples
+      The tags correspond to short and specific sequences added on the 5' end of each primer to distinguish the different samples
     
 - the file containing the reference database in fasta format:
 
     * ``db_v05_r117.fasta``
-    This reference database has been extracted from the release 117 of EMBL using :doc:`ecoPCR <scripts/ecoPCR>`
+      This reference database has been extracted from the release 117 of EMBL using :doc:`ecoPCR <scripts/ecoPCR>`
     
 - the NCBI taxonomy formatted in the :doc:`ecoPCR <scripts/ecoPCR>` format (see the :doc:`obiconvert <scripts/obiconvert>` utility for details) :
 
@@ -191,7 +191,7 @@ it is convenient to work with uniq *sequences* instead of *reads*. To *dereplica
 | 2. group strictly identical reads together                  |
 | 3. output the sequence for each group and its count in the  |
 |    original dataset (in this way, all duplicated reads are  |
-|    removed)                                  |
+|    removed)                                                 |
 |                                                             |
 | Definition adapted from [#]_                                |
 +-------------------------------------------------------------+
@@ -225,6 +225,7 @@ The first sequence record of ``wolf.ali.ngs.uniq.fasta`` is:
 The run of :doc:`obiuniq <scripts/obiuniq>` has added two key=values entries in the header of the fasta sequence :
    - :py:mod:`merged_sample={'29a_F260619': 1}` : this sequence have been found once in a single sample
    - :py:mod:`count=1` : the total number of counts for this sequence is 1 
+   
 To keep only these two ``key=value`` informations, we can use the :doc:`obiannotate <scripts/obiannotate>` command: