.. _references:

References
##############

.. contents::

Assembly and contigs related
-----------------------------

.. automodule:: sequana.assembly
    :members:
    :undoc-members:

.. automodule:: sequana.contigs
    :members:
    :undoc-members:


BAMTOOLS related
--------------------
.. automodule:: sequana.bamtools
    :members:
    :undoc-members:

Coverage (bedtools module)
---------------------------
.. automodule:: sequana.bedtools
    :members:
    :undoc-members:

CIGAR tools
---------------

.. automodule:: sequana.cigar
   :members:
   :undoc-members:

Coverage (theoretical)
--------------------------
.. automodule:: sequana.coverage
    :members:
    :undoc-members:

Access to online database (e.g. ENA)
----------------------------------------
.. automodule:: sequana.databases
    :members:
    :undoc-members:

Enrichment
----------
.. automodule:: sequana.enrichment
    :members:
    :undoc-members:


Experimental design
----------------------------

.. automodule:: sequana.iem
    :members:
    :undoc-members:

FASTQ module
---------------
.. automodule:: sequana.fastq
    :members:
    :undoc-members:

FASTA module
---------------
.. automodule:: sequana.fasta
    :members:
    :undoc-members:

Feature counts module
----------------------
.. automodule:: sequana.featurecounts
    :members:
    :undoc-members:

Sequence and genomic modules
----------------------------------
.. automodule:: sequana.sequence
    :members:
    :undoc-members:

.. automodule:: sequana.codon
    :members:
    :undoc-members:


Kmer module
---------------
.. automodule:: sequana.kmer
    :members:
    :undoc-members:


Taxonomy related (Kraken - Krona)
------------------------------------
.. automodule:: sequana.kraken.analysis
    :members:
    :undoc-members:

.. automodule:: sequana.kraken.multikraken
    :members:
    :undoc-members:


.. automodule:: sequana.taxonomy
    :members:
    :undoc-members:

Pacbio module
----------------
.. automodule:: sequana.pacbio
    :members:
    :undoc-members:
    :inherited-members:

Phred quality
------------------
.. automodule:: sequana.phred
    :members:
    :undoc-members:

RiboDesigner
------------
.. automodule:: sequana.ribodesigner
    :members:
    :undoc-members:

RNAdiff
-------

.. automodule:: sequana.rnadiff
    :members:
    :undoc-members:

.. automodule:: sequana.compare
    :members:
    :undoc-members:

Running median
---------------------
.. automodule:: sequana.running_median
    :members:
    :undoc-members:



Snpeff module
-----------------
.. automodule:: sequana.snpeff
    :members:
    :undoc-members:

General tools
-----------------
.. automodule:: sequana.misc
    :members:
    :undoc-members:

.. automodule:: sequana.tools
    :members:
    :undoc-members:


Peaks
-----

.. automodule:: sequana.macs3
    :members:
    :undoc-members:


Format IO
------------

.. automodule:: sequana.bed
    :members:
    :undoc-members:

.. automodule:: sequana.gff3
    :members:
    :undoc-members:


VCF module
------------
.. automodule:: sequana.freebayes_vcf_filter
    :members:
    :undoc-members:

Module Reports
-------------------

.. automodule:: sequana.modules_report.base_module
    :members:
    :undoc-members:
.. automodule:: sequana.modules_report.bamqc
    :members:
    :undoc-members:
.. automodule:: sequana.modules_report.coverage
    :members:
    :undoc-members:

Wrapper to other tools
-------------------------

.. automodule:: sequana.itol
    :members: 
    :undoc-members:

.. automodule:: sequana.cnv
    :members: 
    :undoc-members:

.. automodule:: sequana.canu_scanner
    :members: 
    :undoc-members:

.. automodule:: sequana.demultiplex
    :members: 
    :undoc-members:

.. automodule:: sequana.trf
    :members: 
    :undoc-members:


Misc
---------

.. automodule:: sequana.datatools
    :members:
    :undoc-members:

.. automodule:: sequana.resources.data
    :members:
    :undoc-members:

.. automodule:: sequana.sniffer
    :members:
    :undoc-members:

.. automodule:: sequana.utils.datatables_js
    :members:
    :undoc-members: