sequana 0.17.3

Description:

sequana 0.17.3

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): 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 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








Not required

sequana-wrappers
Set of wrappers to build pipelines
Not on pypi




Not required

demultiplex
Demultiplex your raw data








License restriction

denovo
denovo sequencing data













fastqc
Get Sequencing Quality control













LORA
Map sequences on target genome













mapper
Map sequences on target genome













nanomerge
Merge barcoded (or unbarcoded) nanopore fastq and reporting













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








Not required

depletion
remove/select reads mapping a reference













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



0.17.3

CHANGES: fix https://github.com/sequana/rnaseq/issues/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.



0.17.2

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



0.17.1

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



0.17.0

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



0.16.9

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.



0.16.8

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



0.16.7

Stable release (fix doc), deprecated.



0.16.6

Refactor IEM to make it more robust with more tests.



0.16.5

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)



0.16.4

hot fixes on RNAdiff reports and enrichments



0.16.3

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)



0.16.2

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



0.16.1

hotfix missing module



0.16.0

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)



0.15.4

add plot for rnaseq/rnadiff



0.15.3

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



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



0.15.1

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



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

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



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.X

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