sequana 0.14.3

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.

Pipelines and tools available in the Sequana project

name/github	description	Latest Pypi version	Test passing
sequana_pipetools	Create and Manage Sequana pipeline
sequana-wrappers	Set of wrappers to build pipelines	Not on pypi
demultiplex	Demultiplex your raw data
fastqc	Get Sequencing Quality control
mapper	Map sequences on target genome
pacbio_qc	Pacbio quality control
ribofinder	Find ribosomal content
rnaseq	RNA-seq analysis
variant_calling	Variant Calling
multicov	Coverage (mapping)
laa	Long read Amplicon Analysis
revcomp	reverse complement of sequence data
downsampling	downsample sequencing data

Pipelines not yet released

name/github	description	Latest Pypi version	Test passing
trf	Find repeats
multitax	Taxonomy analysis

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:

Changelog

Version	Description
0.14.3	new fisher metric in variant calling ability to use several feature in rnaseq/rnadiff pin several libaries due to regression during installs
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	remove some rules now in https://github.com/sequana/sequana-wrappers
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