Package: sequana
How to cite:Citations are important for us to carry on developments.
For Sequana library (including the pipelines), please useCokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of
Open Source Software, 2(16), 352,JOSS DOI doi:10.21105/joss.00352For thegenome coveragetool (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/giy110Also available on bioRxiv (DOI:http://biorxiv.org/content/early/2016/12/08/092478)ForSequanix: 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/bty034Also available on bioRxiv (DOI:https://doi.org/10.1101/162701)Sequanaincludes a set of pipelines related to NGS (new generation sequencing) including quality control, variant calling, coverage, taxonomy, transcriptomics. We also shipSequanix, a graphical user interface for Snakemake pipelines.Pipelines and tools available in the Sequana projectname/githubdescriptionLatest Pypi versionTest passingapptainerssequana_pipetoolsCreate and Manage Sequana pipelineNot requiredsequana-wrappersSet of wrappers to build pipelinesNot on pypiNot requireddemultiplexDemultiplex your raw dataLicense restrictiondenovodenovo sequencing datafastqcGet Sequencing Quality controlLORAMap sequences on target genomemapperMap sequences on target genomenanomergeMerge barcoded (or unbarcoded) nanopore fastq and reportingpacbio_qcPacbio quality controlribofinderFind ribosomal contentrnaseqRNA-seq analysisvariant_callingVariant CallingmulticovCoverage (mapping)laaLong read Amplicon Analysisrevcompreverse complement of sequence datadownsamplingdownsample sequencing dataNot requireddepletionremove/select reads mapping a referencePipelines not yet releasedname/githubdescriptionLatest Pypi versionTest passingtrfFind repeatsmultitaxTaxonomy analysisPlease see thedocumentationfor an
up-to-date status and documentation.ContributorsMaintaining Sequana would not have been possible without users and contributors.
Each contribution has been an encouragement to pursue this project. Thanks to all:ChangelogVersionDescription0.16.9Major fix on PCA and add batch effect plots in RNAdiff analysiscount matrix and DESeq2 output files’ headers fixed with missing index
(no impact on analysis but only for those willing to use the CSV files
in excel)Taxonomy revisited to save taxonomy.dat in gzipped CSV format.0.16.8update IEM for more testingbetter handling of error in RNADiffAdd new methods for ribodesigner0.16.7Stable release (fix doc), deprecated.0.16.6Refactor IEM to make it more robust with more tests.0.16.5refactor to use pyproject instead of setuptoolsremove pkg_resources (future deprecation)remove unused requirements (cookiecutter, adjusttext, docutuils, mock,
psutil, pykwalify)cleanup resources (e.g. moving canvas/bar.py into viz)0.16.4hot fixes on RNAdiff reports and enrichments0.16.3Remove all rules (seehttps://github.com/sequana/sequana-wrappers)
insteadadd precommit for developers and applied to all modules and docFix wrong import for sequana standalone (regression)0.16.2save coverage PNG image (regression)Update taxonomy/coverage standalone (regression) and more tests0.16.1hotfix missing module0.16.0add mpileup modulehomogenization enrichment + fixup rnadiffComplete refactoring of sequana coverage module.
Allow sequana_coverage to handle small eukaryotes in a more memory
efficient way.use click for the sequana_taxonomy and sequana_coverage and
sequana rnadiff commandSmall fixup on homer, idr and phantom modules (for chipseq pipeline)0.15.4add plot for rnaseq/rnadiff0.15.3add sequana.viz.plotly module. use tqdm in bamtools moduleKEGG API changed. We update sequana to use headless server and keep
the feature of annotated and colored pathway.Various improvements on KEGG enrichment including saving pathways,
addition –comparison option in sequana sub-command, plotly plots, etc0.15.2ribodesigner can now accept an input fasta with no GFF assuming the
fasta already contains the rRNA sequencesFix IEM module when dealing with double indexingFix anchors in HTML reports (rnadiff module)refactorise compare module to take several rnadiff results as inputenrichment improvements (export KEGG and GO as csv files0.15.1Fix creation of images directory in modules reportadd missing test related to gffFix #8040.15.0add logo in reportsRNADiff reports can now use shrinkage or not (optional)remove useless rules now in sequana-wrappersupdate main README to add LORA in list of pipelinesLog2FC values are nowshrinked log2FCvalues in volcano plot
and report table. “NotShrinked” columns for Log2FC and Log2FCSE
prior shrinkage are displayed in report table.0.14.6add 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 analysisadd phantom module to compute phantom peaksadd homer module to read annotation files from annotatePeaks0.14.5move start_pipeline standalone inhttps://github.com/sequana/sequana_pipetoolsupdate snpeff module to allows build command to have options0.14.4hotfix bug on kegg colorised pathwaysFix the hover_name in rnadiff volcano plot to include the
index/attribute.pin snakemake to be >=7.160.14.3new fisher metric in variant callingability to use several feature in rnaseq/rnadiffpin several libaries due to regression during installs0.14.2Update ribodesigner0.14.1Kegg enrichment: add gene list ‘all’ and fix incomplete annotation caseNew uniprot module for GO term enrichment and enrichment
refactorisation (transparent for users)0.14.0pinned click>=8.1.0 due to API change (autocomplete)moved tests around to decrease packaging from 16 to 4Mbribodesigner: new plots, clustering and notebook0.13.XRemove useless standalones or moved to mainsequanacommandMove sequana_lane_merging into a subcommand (sequana lane_merging)General cleanup of documentation, test and links to pipelinesadd new ribodesigner subcommand0.12.7Fix memory leak in len() of FastA class0.12.6remove some rules now inhttps://github.com/sequana/sequana-wrappers0.12.5refactorisation of VCF tools/modules to use vcfpy instead of pyVCF0.12.4complete change log before 0.12.4 in the github /doc/Changelog.txt