Sequana documentation
##########################################

|release|

.. include:: ../README.rst


What is Sequana?
================

**Sequana** is a versatile bioinformatics tool that provides:

#. A Python library dedicated to NGS analysis (file-format wrappers, plots,
   coverage, taxonomy, enrichment, RNA-seq, …).
#. A family of :ref:`pipelines <pipelines>` based on
   `Snakemake <https://snakemake.readthedocs.io>`_, each living in its own
   GitHub repository.
#. A set of :ref:`standalone applications <applications>`:
    #. :ref:`sequana_coverage <standalone_sequana_coverage>` — genome coverage
       analysis with confidence intervals.
    #. :ref:`sequana_taxonomy <standalone_sequana_taxonomy>` — quick taxonomy
       on a FastQ file (Kraken + Krona).
    #. ~30 other utility sub-commands grouped under the top-level ``sequana``
       CLI (see :ref:`applications`).

Pipelines cover NGS quality control, variant calling, coverage analysis,
taxonomy, de-novo assembly, :ref:`RNA-seq <pipeline_rnaseq>`,
:ref:`variant calling <pipeline_vc>` and more — see the :ref:`pipelines`
catalogue.

**Sequana** can be used either as a Python library (developers, library users)
or via its pipelines and standalones (end users). To join the project, please
let us know on `github <https://github.com/sequana/sequana/issues/306>`__.


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   <div id="index-grid" class="section group">
   <div class="col span_1_of_3">
        <h3><a href="installation.html">Installation</a></h3>
        <p>pip install sequana</p>
        <h3><a href="auto_examples/index.html">Examples</a></h3>
        <p>Visit our example gallery to use the Python library</p>
        <h3><a href="pipelines.html">NGS pipelines</a></h3>
        <p>Browse the Snakemake pipelines</p>
        <h3><a href="applications.html">Standalone applications</a></h3>
        <p>The sequana CLI and its sub-commands</p>
    </div>
    <div class="col span_2_of_3">
    <div class="jcarousel-wrapper">
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* |coverage|
* |fastqc|
* |kraken|
* |bam|
* |pacbio|

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.. _quick_start:


.. toctree::
    :caption: Pipeline users
    :maxdepth: 2

    installation
    pipeline_user_guide
    pipelines
    tutorial
    case_examples
    faqs

.. toctree::
    :caption: Library users
    :maxdepth: 2

    userguide
    auto_examples/index
    notebooks
    cli_reference

.. toctree::
    :caption: Reference & developers
    :maxdepth: 2

    developers
    applications
    sequanix
    wrappers
    references
    glossary


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`