SEQUANA ############

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:How to cite: Citations are important for us to carry on developments. For Sequana library (including the pipelines), please use

Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of
Open Source Software, 2(16), 352, `JOSS DOI doi:10.21105/joss.00352 <https://joss.theoj.org/papers/10.21105/joss.00352>`_

For the **genome coverage** tool (sequana_coverage):  Desvillechabrol et al, 2018:
detection and characterization of genomic variations using running median and
mixture models. GigaScience, 7(12), 2018. https://doi.org/10.1093/gigascience/giy110

For **Sequanix**: Desvillechabrol et al.
Sequanix: A Dynamic Graphical Interface for Snakemake Workflows
Bioinformatics, bty034, https://doi.org/10.1093/bioinformatics/bty034
Also available on bioRxiv (DOI: https://doi.org/10.1101/162701)

🔧 Overview and Installation

Sequana is a Python library dedicated to bioinformatics. It is also a project that includes a set of pipelines related to NGS (new generation sequencing) including quality control, variant calling, coverage, taxonomy, transcriptomics. We also ship Sequanix, a graphical user interface for Snakemake pipelines.

Pipelines and related projects

Here is a non-exhaustive list of tools and pipelines from the project, with users and developers audience.

.. list-table:: :widths: 15 35 20 15 15 :header-rows: 1

* - **name/github**
  - **description**
  - **Latest Pypi version**
  - **Test passing**
  - **apptainers**
* - `sequana_pipetools <https://github.com/sequana/sequana_pipetools>`_
  - Create and Manage Sequana pipeline
  - .. image:: https://badge.fury.io/py/sequana-pipetools.svg
        :target: https://pypi.python.org/pypi/sequana_pipetools
  - .. image:: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml
  -  Not required
* - `sequana-wrappers <https://github.com/sequana/sequana-wrappers>`_
  - Set of wrappers to build pipelines
  - .. image:: https://badge.fury.io/py/sequana-wrappers.svg
        :target: https://pypi.python.org/pypi/sequana-wrappers
  - .. image:: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml
  - Not required
* - `demultiplex <https://github.com/sequana/demultiplex>`_
  - Demultiplex your raw data
  - .. image:: https://badge.fury.io/py/sequana-demultiplex.svg
        :target: https://pypi.python.org/pypi/sequana-demultiplex
  - .. image:: https://github.com/sequana/demultiplex/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/demultiplex/actions/workflows/main.yml
  - License restriction
* - `denovo <https://github.com/sequana/denovo>`_
  - denovo sequencing data
  - .. image:: https://badge.fury.io/py/sequana-denovo.svg
        :target: https://pypi.python.org/pypi/sequana-denovo
  - .. image:: https://github.com/sequana/denovo/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/denovo/actions/workflows/main.yml
  - .. image:: https://github.com/sequana/denovo/actions/workflows/apptainer.yml/badge.svg
        :target: https://github.com/sequana/denovo/actions/workflows/apptainer.yml
* - `fastqc <https://github.com/sequana/fastqc>`_
  - Get Sequencing Quality control
  - .. image:: https://badge.fury.io/py/sequana-fastqc.svg
        :target: https://pypi.python.org/pypi/sequana-fastqc
  - .. image:: https://github.com/sequana/fastqc/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/fastqc/actions/workflows/main.yml
  - .. image:: https://github.com/sequana/fastqc/actions/workflows/apptainer.yml/badge.svg
        :target: https://github.com/sequana/fastqc/actions/workflows/apptainer.yml
* - `LORA <https://github.com/sequana/lora>`_
  - Map sequences on target genome
  - .. image:: https://badge.fury.io/py/sequana-lora.svg
        :target: https://pypi.python.org/pypi/sequana-lora
  - .. image:: https://github.com/sequana/lora/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/lora/actions/workflows/main.yml
  - .. image:: https://github.com/sequana/lora/actions/workflows/apptainer.yml/badge.svg
        :target: https://github.com/sequana/lora/actions/workflows/apptainer.yml
* - `mapper <https://github.com/sequana/mapper>`_
  - Map sequences on target genome
  - .. image:: https://badge.fury.io/py/sequana-mapper.svg
        :target: https://pypi.python.org/pypi/sequana-mapper
  - .. image:: https://github.com/sequana/mapper/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/mapper/actions/workflows/main.yml
  - .. image:: https://github.com/sequana/mapper/actions/workflows/apptainer.yml/badge.svg
        :target: https://github.com/sequana/mapper/actions/workflows/apptainer.yml
* - `nanomerge <https://github.com/sequana/nanomerge>`_
  - Merge barcoded (or unbarcoded) nanopore fastq and reporting
  - .. image:: https://badge.fury.io/py/sequana-nanomerge.svg
        :target: https://pypi.python.org/pypi/sequana-nanomerge
  - .. image:: https://github.com/sequana/nanomerge/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/nanomerge/actions/workflows/main.yml
  - .. image:: https://github.com/sequana/nanomerge/actions/workflows/apptainer.yml/badge.svg
        :target: https://github.com/sequana/nanomerge/actions/workflows/apptainer.yml
* - `pacbio_qc <https://github.com/sequana/pacbio_qc>`_
  - Pacbio quality control
  - .. image:: https://badge.fury.io/py/sequana-pacbio-qc.svg
        :target: https://pypi.python.org/pypi/sequana-pacbio-qc
  - .. image:: https://github.com/sequana/pacbio_qc/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/pacbio_qc/actions/workflows/main.yml
  - .. image:: https://github.com/sequana/pacbio_qc/actions/workflows/apptainer.yml/badge.svg
        :target: https://github.com/sequana/pacbio_qc/actions/workflows/apptainer.yml
* - `ribofinder <https://github.com/sequana/ribofinder>`_
  - Find ribosomal content
  - .. image:: https://badge.fury.io/py/sequana-ribofinder.svg
        :target: https://pypi.python.org/pypi/sequana-ribofinder
  - .. image:: https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/ribofinder/actions/workflows/main.yml
  - .. image:: https://github.com/sequana/ribofinder/actions/workflows/apptainer.yml/badge.svg
        :target: https://github.com/sequana/ribofinder/actions/workflows/apptainer.yml
* - `rnaseq <https://github.com/sequana/rnaseq>`_
  - RNA-seq analysis
  - .. image:: https://badge.fury.io/py/sequana-rnaseq.svg
        :target: https://pypi.python.org/pypi/sequana-rnaseq
  - .. image:: https://github.com/sequana/rnaseq/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/rnaseq/actions/workflows/main.yml
  - .. image:: https://github.com/sequana/rnaseq/actions/workflows/apptainer.yml/badge.svg
        :target: https://github.com/sequana/rnaseq/actions/workflows/apptainer.yml
* - `variant_calling <https://github.com/sequana/variant_calling>`_
  - Variant Calling
  - .. image:: https://badge.fury.io/py/sequana-variant-calling.svg
        :target: https://pypi.python.org/pypi/sequana-variant-calling
  - .. image:: https://github.com/sequana/variant_calling/actions/workflows/main.yml/badge.svg
        :target: https://github.com/sequana/variant_calling/actions/workflows/main.yml
  - .. image:: https://github.com/sequana/variant_calling/actions/workflows/apptainer.yml/badge.svg
        :target: https://github.com/sequana/variant_calling/actions/workflows/apptainer.yml
* - `multicov <https://github.com/sequana/multicov>`_
  - Coverage (mapping)