Project description
- 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 |
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Not required |
sequana-wrappers |
Set of wrappers to build pipelines |
Not on pypi |
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Not required |
demultiplex |
Demultiplex your raw data |
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License restriction |
denovo |
denovo sequencing data |
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fastqc |
Get Sequencing Quality control |
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LORA |
Map sequences on target genome |
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mapper |
Map sequences on target genome |
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nanomerge |
Merge barcoded (or unbarcoded) nanopore fastq and reporting |
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pacbio_qc |
Pacbio quality control |
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ribofinder |
Find ribosomal content |
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rnaseq |
RNA-seq analysis |
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variant_calling |
Variant Calling |
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multicov |
Coverage (mapping) |
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laa |
Long read Amplicon Analysis |
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revcomp |
reverse complement of sequence data |
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downsampling |
downsample sequencing data |
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Not required |
depletion |
remove/select reads mapping a reference |
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Pipelines not yet released
name/github |
description |
Latest Pypi version |
Test passing |
trf |
Find repeats |
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multitax |
Taxonomy analysis |
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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 |
0.15.2 |
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
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0.15.1 |
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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.
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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
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0.14.5 |
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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
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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
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0.14.2 |
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0.14.1 |
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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
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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
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0.12.7 |
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0.12.6 |
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0.12.5 |
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0.12.4 |
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