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A set of standalone application and pipelines dedicated to NGS (new generation sequencing) analysis

Project description Documentation Status JOSS (journal of open source software) DOI
Python version:

3.7, 3.8, 3.9


On readthedocs


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

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, Also available on bioRxiv (DOI:

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.

Pipelines and tools available in the Sequana project
pipeline or tools Latest Pypi version Test passing Not on pypi

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


Maintaining BioServices would not have been possible without users and contributors. Each contribution has been an encouragement to pursue this project. Thanks to all:


Version Description
  • pinned click>=8.1.0 due to API change (autocomplete)
  • moved tests around to decrease packaging from 16 to 4Mb
  • ribodesigner: new plots, clustering and notebook
  • Remove useless standalones or moved to main sequana command
  • Move sequana_lane_merging into a subcommand (sequana lane_merging)
  • General cleanup of documentation, test and links to pipelines
  • add new ribodesigner subcommand
  • Fix memory leak in len() of FastA class
  • refactorisation of VCF tools/modules to use vcfpy instead of pyVCF
  • complete change log before 0.12.4 on

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sequana-0.14.0.tar.gz (1.5 MB view hashes)

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