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 Sequana 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

0.14.2

  • Update ribodesigner

0.14.1

  • Kegg enrichment: add gene list ‘all’ and fix incomplete annotation case

  • New uniprot module for GO term enrichment and enrichment refactorisation (transparent for users)

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

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.23)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for cokelaer from gravatar.com cokelaer

Credits

Author/Maintainer: Thomas Cokelaer

License

BSD License (new BSD)

Tags

NGS snakemake

Classifiers

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0.23

0.22

0.21.2

0.21.1

0.21.0

0.20.0

0.19.6

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0.19.4

0.19.3

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0.19.1

0.19.0

0.18.0

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0.17.1

0.17.0

0.16.11

0.16.10

0.16.9

0.16.8

0.16.7

0.16.6

0.16.5

0.16.4

0.16.3

0.16.2

0.16.1

0.16.0

0.15.4

0.15.3

0.15.2

0.15.1

0.15.0

0.14.6

0.14.5

0.14.4

0.14.3

This release

0.14.2

0.14.1

0.14.0

0.13.2

0.13.1

0.13.0

0.12.7

0.12.6

0.12.5

0.12.4

0.12.3

0.12.2

0.12.1

0.12.0

0.11.1

0.11.0

0.10.0

0.9.8

0.9.7

0.9.6

0.9.5

0.9.4

0.9.3

0.9.2

0.9.1

0.9.0

0.8.6

0.8.5

0.8.4

0.8.3

0.8.2

0.8.1

0.8.0

0.7.1

0.7.0

0.6.5.post3

0.6.5.post2

0.6.5.post1

0.6.4

0.6.3.post1

0.6.3

0.6.2

0.6.1

0.6.0

0.5.2

0.5.1

0.5.0

0.4.2

0.4.1

0.4.0

0.3.0

0.2.1

0.2.0

0.1.21

0.1.20

0.1.19

0.1.18

0.1.17.1

0.1.16

0.1.15

0.1.14

0.1.13

0.1.12

0.1.11

0.1.10

0.1.9

0.1.8

0.1.7

0.1.6

0.1.5

0.1.4

0.1.2

0.1.1

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0.0.2

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