Sequana documentation

Current version: 0.12.5, Oct 19, 2021

SEQUANA

https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square) https://badge.fury.io/py/sequana.svg https://github.com/sequana/sequana/actions/workflows/main.yml/badge.svg?branch=master https://coveralls.io/repos/github/sequana/sequana/badge.svg?branch=master Documentation Status JOSS (journal of open source software) DOI
Python version

3.7, 3.8, 3.9

Documentation

On readthedocs

Issues

On github

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

For the genome coverage tool (sequana_coverage): Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer http://biorxiv.org/content/early/2016/12/08/092478

For Sequanix: Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer. 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)

Sequana 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.

pipeline or tools

Latest Pypi verison

Test passing

https://github.com/sequana/sequana_pipetools

pipetools_pypi

pipetools_test

https://github.com/sequana/sequana-wrappers

not on pypi

wrappers_test

https://github.com/sequana/demultiplex

demultiplex_pypi

demultiplex_test

https://github.com/sequana/fastqc

fastqc_pypi

fastqc_test

https://github.com/sequana/mapper

mapper_pypi

mapper_test

https://github.com/sequana/ribofinder

ribo_pypi

ribo_test

https://github.com/sequana/rnaseq

rnaseq_pypi

rnaseq_test

Please see the documentation for an up-to-date status and documentation.

Changelog

Version

Description

0.12.5

  • refactorisation of VCF tools/modules to use vcfpy instead of pyVCF

0.12.4

  • complete change log before 0.12.4 on readthedocs.org

What is Sequana ?

Sequana is a versatile tool that provides

  1. A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats).

  2. A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable rules (see Rules).

  3. Original tools to help in the creation of such pipelines including HTML reports.

  4. Standalone applications:
    1. sequana_coverage ease the extraction of genomic regions of interest and genome coverage information

    2. sequana_taxonomy performs a quick taxonomy of your FastQ. This requires dedicated databases to be downloaded.

    3. Sequanix: GUI for snakemake workflows, a GUI for Snakemake workflows (hence Sequana pipelines as well)

The sequana pipelines are various. Since March 2020, they have their own independent life within dedicated github repositories. You may find pipelines for NGS quality control (e.g. adapters removal, phix removal, trimming of bad quality bases), variant calling, characterisation of the genome coverage, taxonomic classification, de-novo assembly, Variant calling, RNA-seq, etc. See the Pipelines section for more information.

Sequana can be used by developers to create new pipelines and by users in the form of applications ready for production. Moreover, Sequanix can be used to set the parameters of pipelines and execute them easily with a graphical user interface.

To join the project, please let us know on github.

Installation

conda install sequana

Examples

Visit our example gallery to use the Python library

NGS pipelines

Learn about available Snakemake pipelines

Standalone applications

Standalone applications including Sequanix (GUI for snakemake) and the sequana_coverage tool.

User guide and reference