sequana 0.12.7

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

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
https://github.com/sequana/sequana-wrappers	not on pypi
https://github.com/sequana/demultiplex
https://github.com/sequana/fastqc
https://github.com/sequana/mapper
https://github.com/sequana/pacbio_qc
https://github.com/sequana/ribofinder
https://github.com/sequana/rnaseq

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