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

Project description

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.

Pipelines and tools available in the Sequana project
pipeline or tools Latest Pypi version Test passing
https://github.com/sequana/sequana_pipetools https://badge.fury.io/py/sequana-pipetools.svg https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml/badge.svg
https://github.com/sequana/sequana-wrappers Not on pypi https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml/badge.svg
https://github.com/sequana/demultiplex https://badge.fury.io/py/sequana-demultiplex.svg https://github.com/sequana/demultiplex/actions/workflows/main.yml/badge.svg
https://github.com/sequana/fastqc https://badge.fury.io/py/sequana-fastqc.svg https://github.com/sequana/fastqc/actions/workflows/main.yml/badge.svg
https://github.com/sequana/mapper https://badge.fury.io/py/sequana-mapper.svg https://github.com/sequana/mapper/actions/workflows/main.yml/badge.svg
https://github.com/sequana/pacbio_qc https://badge.fury.io/py/sequana-pacbio-qc.svg https://github.com/sequana/pacbio_qc/actions/workflows/main.yml/badge.svg
https://github.com/sequana/ribofinder https://badge.fury.io/py/sequana-ribofinder.svg https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg
https://github.com/sequana/rnaseq https://badge.fury.io/py/sequana-rnaseq.svg https://github.com/sequana/rnaseq/actions/workflows/main.yml/badge.svg
https://github.com/sequana/variant_calling https://badge.fury.io/py/sequana-variant-calling.svg https://github.com/sequana/variant_calling/actions/workflows/main.yml/badge.svg

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

Contributors

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

https://contrib.rocks/image?repo=sequana/sequana

Changelog

Version Description
0.14.0
  • 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
0.13.X
  • 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
0.12.7
  • Fix memory leak in len() of FastA class
0.12.6
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

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

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