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/pacbio_qc

pacbio_qc_pypi

pacbio_qc_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

0.12.7

  • Fix memory leak in len() of FastA class

0.12.6

  • remove some useless rules

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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Release history Release notifications | RSS feed

0.23

0.22

0.21.2

0.21.1

0.21.0

0.20.0

0.19.6

0.19.5

0.19.4

0.19.3

0.19.2

0.19.1

0.19.0

0.18.0

0.17.3

0.17.2

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

0.14.2

0.14.1

0.14.0

0.13.2

0.13.1

0.13.0

This release

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

0.1.0

0.0.3

0.0.2

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