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Showing content from https://github.com/sequana/sequana below:

sequana/sequana: Sequana: a set of Snakemake NGS pipelines

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): Desvillechabrol et al, 2018: detection and characterization of genomic variations using running median and mixture models. GigaScience, 7(12), 2018. https://doi.org/10.1093/gigascience/giy110

For Sequanix: Desvillechabrol et al. 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 is a Python library dedicated to bioinformatics. It is also a project that 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.

Here is a non exahustive list of tools and pipelines from the project. with users and developers audience.

Please see the documentation for an up-to-date status and documentation.

Maintaining Sequana would not have been possible without users and contributors. Each contribution has been an encouragement to pursue this project. Thanks to all:

• NEW new modules related to genomic metrics (zdna, imotif, cruciform,etc)
• NEW new visualisation tools
• NEW parser for hmmtools

• update pyproject with matploblib, scipy, and all dependencie except snakemake (keep <8.X and its pulp dependency <2.8) because 8.X breaks the containers and therefore all pipelines. no workaround. we will need a snakemake 'frozen library'. This is unfortunate.
• CHANGES: remove multiqc plugin quality_control (obsolet) and updated many plugin due to increased version ofmultiqc.

• UPDATE pyproject layout to be poetry2.0 compatible. drop support py3.8
• NEW: kozak module, somy score, telomere, biomol, rnafold, restriction enzyme
• UPDATES: sequence module has more metrics (e.g. karlin signature), fastq has a histogram for long reads,

• NEW: somy scores (module and standalone)
• CHANGES: coverage now uses mosdepth for the bam2cov. can also handle creation of the 4-column coverage file from BAM on the fly.
• Drop python 3.8 support (more and more dependencies issues)

• CHANGES: fix sequana/rnaseq#45 to better handle multiqc files especially, feature counts plugin. Fix #855 to be able to name batch effect column arbitrary to any name. Fix batch effect column (and all others) to be strings rather than integer. If integer, factor are sorted based on the integer values, not the factor itself.
• NEWS: add size factor comments and table.

• Pin down pulp<2.8 and snakemake to <8.0 (too many changes in snakemake)

• NEW: tsne plot
• CHANGES: update iem module with additional specs

• CHANGE. remove the substractor utility (use sequana_depletion pipeline instead)
• CHANGE. remove get_max_gc_correlation function from bedtools. not used.
• CHANGE. Got rid of freebayes_bcf_filter redundant with freebayes_vcf_filter; replace scipy fisher test with own implementation. Remove useless VCF code.
• FIXES. rnadiff HTML report
• IMPROV. speedup kegg enrichment using multiprocess
• IMPROV. sequana_taxonomy can now download toydb and viruses_masking DBs from zenodo
• NEW function to retrieve the GO terms and genes from panther website
• NEW keep_reads function in fastq class
• Major update of the IEM module (renamed IEM class into SampleSheet)
• NEW addW find-integrated-genes standalone

• Major fix on PCA and add batch effect plots in RNAdiff analysis
• count 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.

• update IEM for more testing
• better handling of error in RNADiff
• Add new methods for ribodesigner

• Stable release (fix doc), deprecated.

• Refactor IEM to make it more robust with more tests.

• refactor to use pyproject instead of setuptools
• remove pkg_resources (future deprecation)
• remove unused requirements (cookiecutter, adjusttext, docutuils, mock, psutil, pykwalify)
• cleanup resources (e.g. moving canvas/bar.py into viz)

• hot fixes on RNAdiff reports and enrichments

• Remove all rules (see https://github.com/sequana/sequana-wrappers) instead
• add precommit for developers and applied to all modules and doc
• Fix wrong import for sequana standalone (regression)

• save coverage PNG image (regression)
• Update taxonomy/coverage standalone (regression) and more tests

• hotfix missing module

• add mpileup module
• homogenization enrichment + fixup rnadiff
• Complete 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 command
• Small fixup on homer, idr and phantom modules (for chipseq pipeline)

• add plot for rnaseq/rnadiff

• add sequana.viz.plotly module. use tqdm in bamtools module
• KEGG 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, etc

• ribodesigner can now accept an input fasta with no GFF assuming the fasta already contains the rRNA sequences
• Fix IEM module when dealing with double indexing
• Fix anchors in HTML reports (rnadiff module)
• refactorise compare module to take several rnadiff results as input
• enrichment improvements (export KEGG and GO as csv files

• Fix creation of images directory in modules report
• add missing test related to gff
• Fix #804

• 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.

• 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

• move start_pipeline standalone in https://github.com/sequana/sequana_pipetools
• update snpeff module to allows build command to have options

• 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

• new fisher metric in variant calling
• ability to use several feature in rnaseq/rnadiff
• pin several libaries due to regression during installs

• Update ribodesigner

• Kegg enrichment: add gene list 'all' and fix incomplete annotation case
• New uniprot module for GO term enrichment and enrichment refactorisation (transparent for users)

• 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

• 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

• remove some rules now in https://github.com/sequana/sequana-wrappers
• refactorisation of VCF tools/modules to use vcfpy instead of pyVCF
• complete change log before 0.12.4 in the github /doc/Changelog.txt

Any ❓ Feel free to [open an issue](https://github.com/sequana/sequana/issues)

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