Doc

README.rst

@@ -17,7 +17,6 @@ software.
 * `Issues <https://github.com/compmetagen/micca/issues>`_
 * `Github page <https://github.com/compmetagen/micca>`_
 
-
 Key features:
 
 * supports **single-end** (Roche 454, Illumina MiSeq/HiSeq ,Ion
@@ -48,7 +47,7 @@ ftp://ftp.fmach.it/metagenomics/micca/scirep/.
 micca wraps third party software packages and these **should be
 cited** if they are used:
 
-* VSEARCH (https://github.com/torognes/vsearch) used in ``classify``,
+* VSEARCH (doi: 10.7717/peerj.2584) used in ``classify``,
   ``filter``, ``mergepairs``, ``otu`` and ``msa`` commands
 * MUSCLE (doi: 10.1093/nar/gkh340) used in ``msa`` and ``tree`` commands
 * FastTree (doi: 10.1371/journal.pone.0009490) used in the ``tree`` command

doc/source/index.rst

@@ -5,45 +5,37 @@
 
 .. include:: ../../README.rst
 
-Getting Started
-***************
-
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
+   :caption: Getting Started
 
    install
    run
    databases
 
-Tutorials
-*********
-
 .. toctree::
    :maxdepth: 1
+   :caption: Tutorials
 
    singleend
    pairedend
    phyloseq
    table
    picrust
 
-In Depth
-*********
-
 .. toctree::
    :maxdepth: 1
+   :caption: In Depth
 
    filtering
    otu
    formats
    changes
 
-Command reference
-*****************
-
 .. toctree::
    :glob:
    :maxdepth: 1
+   :caption: Command reference
 
    commands/*
 

doc/source/otu.rst

@@ -27,7 +27,7 @@ The :doc:`commands/otu` command returns in a single directory 5 files:
    otus.fasta
       FASTA containing the representative sequences (OTUs)::
 
-       >DENOVO1
+         >DENOVO1
      	 GACGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGGGG...
      	 >DENOVO2
      	 GATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCA...
@@ -40,8 +40,8 @@ The :doc:`commands/otu` command returns in a single directory 5 files:
       ids::
 
          DENOVO1 IS0AYJS04JQKIS;sample=Mw_01
-	       DENOVO2 IS0AYJS04JL6RS;sample=Mw_01
-	       DENOVO3 IS0AYJS04H4XNN;sample=Mw_01
+	     DENOVO2 IS0AYJS04JL6RS;sample=Mw_01
+	     DENOVO3 IS0AYJS04H4XNN;sample=Mw_01
 	 ...
 
    hits.txt
@@ -50,8 +50,8 @@ The :doc:`commands/otu` command returns in a single directory 5 files:
       identity (if available), see :ref:`otu-definition_identity`::
 
          IS0AYJS04JE658;sample=Mw_01; IS0AYJS04I4XYN;sample=Mw_01 99.4
-	       IS0AYJS04JPH34;sample=Mw_01; IS0AYJS04JVUBC;sample=Mw_01 98.0
-	       IS0AYJS04I67XN;sample=Mw_01; IS0AYJS04JVUBC;sample=Mw_01 99.7
+	     IS0AYJS04JPH34;sample=Mw_01; IS0AYJS04JVUBC;sample=Mw_01 98.0
+	     IS0AYJS04I67XN;sample=Mw_01; IS0AYJS04JVUBC;sample=Mw_01 99.7
 	 ...
 
    otuschim.fasta