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=main https://coveralls.io/repos/github/sequana/sequana/badge.svg?branch=main Documentation Status JOSS (journal of open source software) DOI Python 3.8 | 3.9 | 3.10 GitHub Issues
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. Sequana coverage: detection and characterization of genomic variations using running median and mixture models. GigaScience, 7(12), 2018. https://doi.org/10.1093/gigascience/giy110 Also available on bioRxiv (DOI: 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

apptainers

sequana_pipetools

Create and Manage Sequana pipeline

 https://badge.fury.io/py/sequana-pipetools.svg https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml/badge.svg

sequana-wrappers

Set of wrappers to build pipelines

Not on pypi

 https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml/badge.svg

demultiplex

Demultiplex your raw data

 https://badge.fury.io/py/sequana-demultiplex.svg https://github.com/sequana/demultiplex/actions/workflows/main.yml/badge.svg

denovo

denovo sequencing data

 https://badge.fury.io/py/sequana-denovo.svg https://github.com/sequana/denovo/actions/workflows/main.yml/badge.svg https://github.com/sequana/denovo/actions/workflows/apptainer.yml/badge.svg

fastqc

Get Sequencing Quality control

 https://badge.fury.io/py/sequana-fastqc.svg https://github.com/sequana/fastqc/actions/workflows/main.yml/badge.svg https://github.com/sequana/fastqc/actions/workflows/apptainer.yml/badge.svg

LORA

Map sequences on target genome

 https://badge.fury.io/py/sequana-lora.svg https://github.com/sequana/lora/actions/workflows/main.yml/badge.svg https://github.com/sequana/lora/actions/workflows/apptainer.yml/badge.svg

mapper

Map sequences on target genome

 https://badge.fury.io/py/sequana-mapper.svg https://github.com/sequana/mapper/actions/workflows/main.yml/badge.svg https://github.com/sequana/mapper/actions/workflows/apptainer.yml/badge.svg

pacbio_qc

Pacbio quality control

 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/pacbio_qc/actions/workflows/apptainer.yml/badge.svg

ribofinder

Find ribosomal content

 https://badge.fury.io/py/sequana-ribofinder.svg https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg https://github.com/sequana/ribofinder/actions/workflows/apptainer.yml/badge.svg

rnaseq

RNA-seq analysis

 https://badge.fury.io/py/sequana-rnaseq.svg https://github.com/sequana/rnaseq/actions/workflows/main.yml/badge.svg https://github.com/sequana/rnaseq/actions/workflows/apptainer.yml/badge.svg

variant_calling

Variant Calling

 https://badge.fury.io/py/sequana-variant-calling.svg https://github.com/sequana/variant_calling/actions/workflows/main.yml/badge.svg https://github.com/sequana/variant_calling/actions/workflows/apptainer.yml/badge.svg

multicov

Coverage (mapping)

 https://badge.fury.io/py/sequana-multicov.svg https://github.com/sequana/multicov/actions/workflows/main.yml/badge.svg https://github.com/sequana/coverage/actions/workflows/apptainer.yml/badge.svg

laa

Long read Amplicon Analysis

 https://badge.fury.io/py/sequana-laa.svg https://github.com/sequana/laa/actions/workflows/main.yml/badge.svg

revcomp

reverse complement of sequence data

 https://badge.fury.io/py/sequana-revcomp.svg https://github.com/sequana/revcomp/actions/workflows/main.yml/badge.svg

downsampling

downsample sequencing data

 https://badge.fury.io/py/sequana-downsampling.svg https://github.com/sequana/downsampling/actions/workflows/main.yml/badge.svg
Pipelines not yet released

name/github

description

Latest Pypi version

Test passing

trf

Find repeats

 https://badge.fury.io/py/sequana-trf.svg https://github.com/sequana/trf/actions/workflows/main.yml/badge.svg

multitax

Taxonomy analysis

 https://badge.fury.io/py/sequana-multitax.svg https://github.com/sequana/multitax/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

0.15.0

  • add logo in reports

  • RNADiff reports can now use shrinkage or not (optional)

  • remove useless rules now in sequana-wrappers

  • update main README to add LORA in list of pipelines

  • Log2FC values are now shrinked log2FC values in volcano plot and report table. “NotShrinked” columns for Log2FC and Log2FCSE prior shrinkage are displayed in report table.

0.14.6

  • add fasta_and_gff_annotation module to correct fasta and gff given a vcf file.

  • add macs3 module to read output of macs3 peak detector.

  • add idr module to read results of idr analysis

  • add phantom module to compute phantom peaks

  • add homer module to read annotation files from annotatePeaks

0.14.5

0.14.4

  • hotfix bug on kegg colorised pathways

  • Fix the hover_name in rnadiff volcano plot to include the index/attribute.

  • pin snakemake to be >=7.16

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

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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This release

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0.14.6

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