Compute basic statistics, rarefy and summarize OTU/SV tables using micca
========================================================================

.. note::

    This tutorial requires :doc:`pairedend_97` to be done.

The command :doc:`commands/tablestats` reports a sample summary, an OTU summary
and the rarefaction curves for the input OTU/SV table:

.. code-block:: sh 

    micca tablestats -i denovo_greedy_otus/otutable.txt -o tablestats

Inspecting the file ``tablestats/tablestats_samplesumm.txt`` you can see that
the less abundant sample contains 512 reads::

    Sample          Depth   NOTU    NSingle
    B1114D1-PL1-E4  512     145     68
    B1014D2-PL1-C4  1356    152     57
    B0214D3-PL1-F1  1665    192     74
    ...             ...     ...     ...

.. note::

    Rarefaction curves can be inspected through
    ``tablestats/tablestats_rarecurve.txt`` and
    ``tablestats/tablestats_rarecurve_plot.png``.

To compare different samples, the OTU/SV table must be subsampled (`rarefied
<https://en.wikipedia.org/wiki/Rarefaction_(ecology)>`_) using the command
:doc:`commands/tablerare`. In this case we are interested in rarefy the table
with the depth of the less abundant sample (``B1114D1-PL1-E4``):

.. code-block:: sh

    micca tablerare -i denovo_greedy_otus/otutable.txt -o denovo_greedy_otus/otutable_rare.txt -d 500

Now we can summarize communities by their taxonomic composition. The
:doc:`commands/tabletotax` creates in the output directory a table for each
taxonomic level (``taxtable1.txt``, ..., ``taxtableN.txt``). OTU counts are
summed together if they have the same taxonomy at the considered level.

.. code-block:: sh

    micca tabletotax -i denovo_greedy_otus/otutable_rare.txt -t denovo_greedy_otus/taxa.txt -o taxtables

Finally, we can generate a relative abundance bar plot from generated taxa
tables, using the command :doc:`commands/tablebar`. In this case only the bar
plot relative to the taxonomy level 2 (phylum) will be generated:

.. code-block:: sh
   
    micca tablebar -i taxtables/taxtable2.txt -o taxtables/taxtable2.png

.. image:: /images/garda_taxtable2.png
    :align: center
    :scale: 25%