.. _references_pipelines:

References (pipeline back-ends)
###############################

.. contents::
   :local:

BAM / alignment
===============

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

Coverage
========

.. automodule:: sequana.coverage
    :members:
    :undoc-members:

.. automodule:: sequana.bedtools
    :members:
    :undoc-members:

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

Assembly and contigs
====================

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

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

.. automodule:: sequana.checkm
    :members:
    :undoc-members:

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

Taxonomy
========

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

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

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

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

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

.. automodule:: sequana.krona
    :members:
    :undoc-members:

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

PacBio / IsoSeq / LAA
=====================

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

.. automodule:: sequana.pacbio_amplicon
    :members:
    :undoc-members:

.. automodule:: sequana.isoseq
    :members:
    :undoc-members:

.. automodule:: sequana.laa
    :members:
    :undoc-members:

RNA-seq / counting
==================

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

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

.. automodule:: sequana.featurecounts
    :members:
    :undoc-members:

.. automodule:: sequana.salmon
    :members:
    :undoc-members:

Variants / annotation
=====================

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

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

.. automodule:: sequana.somy
    :members:
    :undoc-members:

ChIP-seq / peak calling
=======================

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

.. automodule:: sequana.homer
    :members:
    :undoc-members:

.. automodule:: sequana.idr
    :members:
    :undoc-members:

.. automodule:: sequana.frip
    :members:
    :undoc-members:

.. automodule:: sequana.phantom
    :members:
    :undoc-members:

Wrappers to other tools
=======================

.. automodule:: sequana.blast
    :members:
    :undoc-members:

.. automodule:: sequana.kegg
    :members:
    :undoc-members:

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

.. automodule:: sequana.orthofinder
    :members:
    :undoc-members:

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

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

.. automodule:: sequana.codeml
    :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.bwa_bam_to_fastq
    :members:
    :undoc-members:

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

.. automodule:: sequana.modules_report.cutadapt
    :members:
    :undoc-members:

.. automodule:: sequana.modules_report.fastqc
    :members:
    :undoc-members:

.. automodule:: sequana.modules_report.fastq_stats
    :members:
    :undoc-members:

.. automodule:: sequana.modules_report.joint_calling
    :members:
    :undoc-members:

.. automodule:: sequana.modules_report.kegg_enrichment
    :members:
    :undoc-members:

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

.. automodule:: sequana.modules_report.multi_summary
    :members:
    :undoc-members:

.. automodule:: sequana.modules_report.pacbio_input_bam
    :members:
    :undoc-members:

.. automodule:: sequana.modules_report.panther_enrichment
    :members:
    :undoc-members:

.. automodule:: sequana.modules_report.phix
    :members:
    :undoc-members:

.. automodule:: sequana.modules_report.quast
    :members:
    :undoc-members:

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

.. automodule:: sequana.modules_report.summary
    :members:
    :undoc-members:

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

.. automodule:: sequana.modules_report.uniprot_enrichment
    :members:
    :undoc-members:

.. automodule:: sequana.modules_report.variant_calling
    :members:
    :undoc-members: