| Name | sequana JSON |
| Version |
0.16.11
JSON |
| download |
| home_page | |
| Summary | A set of standalone application and pipelines dedicated to NGS analysis |
| upload_time | 2024-03-18 15:24:53 |
| maintainer | |
| docs_url | None |
| author | Thomas Cokelaer |
| requires_python | >=3.8,<4.0 |
| license | new BSD |
| keywords |
snakemake
sequana
ngs
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
SEQUANA
############
.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)
:target: http://bioconda.github.io/recipes/sequana/README.html
.. image:: https://badge.fury.io/py/sequana.svg
:target: https://pypi.python.org/pypi/sequana
.. image:: https://github.com/sequana/sequana/actions/workflows/main.yml/badge.svg?branch=main
:target: https://github.com/sequana/sequana/actions/workflows/main.yml
.. image:: https://coveralls.io/repos/github/sequana/sequana/badge.svg?branch=main
:target: https://coveralls.io/github/sequana/sequana?branch=main
.. image:: http://readthedocs.org/projects/sequana/badge/?version=main
:target: http://sequana.readthedocs.org/en/latest/?badge=main
:alt: Documentation Status
.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
:target: http://joss.theoj.org/papers/10.21105/joss.00352
:alt: JOSS (journal of open source software) DOI
.. image:: https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg
:target: https://pypi.python.org/pypi/sequana
:alt: Python 3.8 | 3.9 | 3.10 | 3.11
.. image:: https://img.shields.io/github/issues/sequana/sequana.svg
:target: https://github.com/sequana/sequana/issues
:alt: GitHub Issues
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/psf/black
: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 <https://joss.theoj.org/papers/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.
.. list-table:: Pipelines and tools available in the Sequana project
:widths: 15 35 20 15 15
:header-rows: 1
* - **name/github**
- **description**
- **Latest Pypi version**
- **Test passing**
- **apptainers**
* - `sequana_pipetools <https://github.com/sequana/sequana_pipetools>`_
- Create and Manage Sequana pipeline
- .. image:: https://badge.fury.io/py/sequana-pipetools.svg
:target: https://pypi.python.org/pypi/sequana_pipetools
- .. image:: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml
- Not required
* - `sequana-wrappers <https://github.com/sequana/sequana-wrappers>`_
- Set of wrappers to build pipelines
- Not on pypi
- .. image:: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml
- Not required
* - `demultiplex <https://github.com/sequana/demultiplex>`_
- Demultiplex your raw data
- .. image:: https://badge.fury.io/py/sequana-demultiplex.svg
:target: https://pypi.python.org/pypi/sequana-demultiplex
- .. image:: https://github.com/sequana/demultiplex/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/demultiplex/actions/workflows/main.yml
- License restriction
* - `denovo <https://github.com/sequana/denovo>`_
- denovo sequencing data
- .. image:: https://badge.fury.io/py/sequana-denovo.svg
:target: https://pypi.python.org/pypi/sequana-denovo
- .. image:: https://github.com/sequana/denovo/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/denovo/actions/workflows/main.yml
- .. image:: https://github.com/sequana/denovo/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/denovo/actions/workflows/apptainer.yml
* - `fastqc <https://github.com/sequana/fastqc>`_
- Get Sequencing Quality control
- .. image:: https://badge.fury.io/py/sequana-fastqc.svg
:target: https://pypi.python.org/pypi/sequana-fastqc
- .. image:: https://github.com/sequana/fastqc/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/fastqc/actions/workflows/main.yml
- .. image:: https://github.com/sequana/fastqc/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/fastqc/actions/workflows/apptainer.yml
* - `LORA <https://github.com/sequana/lora>`_
- Map sequences on target genome
- .. image:: https://badge.fury.io/py/sequana-lora.svg
:target: https://pypi.python.org/pypi/sequana-lora
- .. image:: https://github.com/sequana/lora/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/lora/actions/workflows/main.yml
- .. image:: https://github.com/sequana/lora/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/lora/actions/workflows/apptainer.yml
* - `mapper <https://github.com/sequana/mapper>`_
- Map sequences on target genome
- .. image:: https://badge.fury.io/py/sequana-mapper.svg
:target: https://pypi.python.org/pypi/sequana-mapper
- .. image:: https://github.com/sequana/mapper/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/mapper/actions/workflows/main.yml
- .. image:: https://github.com/sequana/mapper/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/mapper/actions/workflows/apptainer.yml
* - `nanomerge <https://github.com/sequana/nanomerge>`_
- Merge barcoded (or unbarcoded) nanopore fastq and reporting
- .. image:: https://badge.fury.io/py/sequana-nanomerge.svg
:target: https://pypi.python.org/pypi/sequana-nanomerge
- .. image:: https://github.com/sequana/nanomerge/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/nanomerge/actions/workflows/main.yml
- .. image:: https://github.com/sequana/nanomerge/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/nanomerge/actions/workflows/apptainer.yml
* - `pacbio_qc <https://github.com/sequana/pacbio_qc>`_
- Pacbio quality control
- .. image:: https://badge.fury.io/py/sequana-pacbio-qc.svg
:target: https://pypi.python.org/pypi/sequana-pacbio-qc
- .. image:: https://github.com/sequana/pacbio_qc/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/pacbio_qc/actions/workflows/main.yml
- .. image:: https://github.com/sequana/pacbio_qc/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/pacbio_qc/actions/workflows/apptainer.yml
* - `ribofinder <https://github.com/sequana/ribofinder>`_
- Find ribosomal content
- .. image:: https://badge.fury.io/py/sequana-ribofinder.svg
:target: https://pypi.python.org/pypi/sequana-ribofinder
- .. image:: https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/ribofinder/actions/workflows/main.yml
- .. image:: https://github.com/sequana/ribofinder/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/ribofinder/actions/workflows/apptainer.yml
* - `rnaseq <https://github.com/sequana/rnaseq>`_
- RNA-seq analysis
- .. image:: https://badge.fury.io/py/sequana-rnaseq.svg
:target: https://pypi.python.org/pypi/sequana-rnaseq
- .. image:: https://github.com/sequana/rnaseq/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/rnaseq/actions/workflows/main.yml
- .. image:: https://github.com/sequana/rnaseq/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/rnaseq/actions/workflows/apptainer.yml
* - `variant_calling <https://github.com/sequana/variant_calling>`_
- Variant Calling
- .. image:: https://badge.fury.io/py/sequana-variant-calling.svg
:target: https://pypi.python.org/pypi/sequana-variant-calling
- .. image:: https://github.com/sequana/variant_calling/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/variant_calling/actions/workflows/main.yml
- .. image:: https://github.com/sequana/variant_calling/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/variant_calling/actions/workflows/apptainer.yml
* - `multicov <https://github.com/sequana/multicov>`_
- Coverage (mapping)
- .. image:: https://badge.fury.io/py/sequana-multicov.svg
:target: https://pypi.python.org/pypi/sequana-multicov
- .. image:: https://github.com/sequana/multicov/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/multicov/actions/workflows/main.yml
- .. image:: https://github.com/sequana/coverage/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/coverage/actions/workflows/apptainer.yml
* - `laa <https://github.com/sequana/laa>`_
- Long read Amplicon Analysis
- .. image:: https://badge.fury.io/py/sequana-laa.svg
:target: https://pypi.python.org/pypi/sequana-laa
- .. image:: https://github.com/sequana/laa/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/laa/actions/workflows/main.yml
- .. image:: https://github.com/sequana/laa/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/laa/actions/workflows/apptainer.yml
* - `revcomp <https://github.com/sequana/revcomp>`_
- reverse complement of sequence data
- .. image:: https://badge.fury.io/py/sequana-revcomp.svg
:target: https://pypi.python.org/pypi/sequana-revcomp
- .. image:: https://github.com/sequana/revcomp/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/revcomp/actions/workflows/main.yml
- .. image:: https://github.com/sequana/revcomp/actions/workflows/apptainer.yml/badge.svg
:target: https://github.com/sequana/revcomp/actions/workflows/apptainer.yml
* - `downsampling <https://github.com/sequana/downsampling>`_
- downsample sequencing data
- .. image:: https://badge.fury.io/py/sequana-downsampling.svg
:target: https://pypi.python.org/pypi/sequana-downsampling
- .. image:: https://github.com/sequana/downsampling/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/downsampling/actions/workflows/main.yml
- Not required
* - `depletion <https://github.com/sequana/depletion>`_
- remove/select reads mapping a reference
- .. image:: https://badge.fury.io/py/sequana-downsampling.svg
:target: https://pypi.python.org/pypi/sequana-depletion
- .. image:: https://github.com/sequana/depletion/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/depletion/actions/workflows/main.yml
-
.. list-table:: Pipelines not yet released
:widths: 20 40 20 20
:header-rows: 1
* - **name/github**
- **description**
- **Latest Pypi version**
- **Test passing**
* - `trf <https://github.com/sequana/trf>`_
- Find repeats
- .. image:: https://badge.fury.io/py/sequana-trf.svg
:target: https://pypi.python.org/pypi/sequana-trf
- .. image:: https://github.com/sequana/trf/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/trf/actions/workflows/main.yml
* - `multitax <https://github.com/sequana/multitax>`_
- Taxonomy analysis
- .. image:: https://badge.fury.io/py/sequana-multitax.svg
:target: https://pypi.python.org/pypi/sequana-multitax
- .. image:: https://github.com/sequana/multitax/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/multitax/actions/workflows/main.yml
**Please see the** `documentation <http://sequana.readthedocs.org>`_ 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:
.. image:: https://contrib.rocks/image?repo=sequana/sequana
:target: https://github.com/sequana/sequana/graphs/contributors
Changelog
~~~~~~~~~
========= ==========================================================================
Version Description
========= ==========================================================================
0.17.0 * viz submodules: remove easydev and cleanup scipy imports
* remove the substractor utility (use sequana_depletion pipeline instead)
* remove get_max_gc_correlation function from bedtools. not used.
* Major change in VCF reader (freebayes). 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
* speedup kegg enrichment using multiprocess
* Allow sequana_taxonomy to download toydb and viruses_masking DBs from
zenodo
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
========= ==========================================================================
Raw data
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"description": "SEQUANA\n############\n\n\n.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)\n :target: http://bioconda.github.io/recipes/sequana/README.html\n\n.. image:: https://badge.fury.io/py/sequana.svg\n :target: https://pypi.python.org/pypi/sequana\n\n.. image:: https://github.com/sequana/sequana/actions/workflows/main.yml/badge.svg?branch=main\n :target: https://github.com/sequana/sequana/actions/workflows/main.yml\n\n.. image:: https://coveralls.io/repos/github/sequana/sequana/badge.svg?branch=main\n :target: https://coveralls.io/github/sequana/sequana?branch=main\n\n.. image:: http://readthedocs.org/projects/sequana/badge/?version=main\n :target: http://sequana.readthedocs.org/en/latest/?badge=main\n :alt: Documentation Status\n\n.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg\n :target: http://joss.theoj.org/papers/10.21105/joss.00352\n :alt: JOSS (journal of open source software) DOI\n\n.. image:: https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg\n :target: https://pypi.python.org/pypi/sequana\n :alt: Python 3.8 | 3.9 | 3.10 | 3.11\n\n.. image:: https://img.shields.io/github/issues/sequana/sequana.svg\n :target: https://github.com/sequana/sequana/issues\n :alt: GitHub Issues\n\n.. image:: https://img.shields.io/badge/code%20style-black-000000.svg\n :target: https://github.com/psf/black\n\n\n:How to cite: Citations are important for us to carry on developments.\n For Sequana library (including the pipelines), please use\n\n Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of\n Open Source Software, 2(16), 352, `JOSS DOI doi:10.21105/joss.00352 <https://joss.theoj.org/papers/10.21105/joss.00352>`_\n\n For the **genome coverage** tool (sequana_coverage): Desvillechabrol et al, 2018:\n detection and characterization of genomic variations using running median and\n mixture models. GigaScience, 7(12), 2018. https://doi.org/10.1093/gigascience/giy110\n\n For **Sequanix**: Desvillechabrol et al.\n Sequanix: A Dynamic Graphical Interface for Snakemake Workflows\n Bioinformatics, bty034, https://doi.org/10.1093/bioinformatics/bty034\n Also available on bioRxiv (DOI: https://doi.org/10.1101/162701)\n\n\n**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.\n\n\n\n.. list-table:: Pipelines and tools available in the Sequana project\n :widths: 15 35 20 15 15\n :header-rows: 1\n\n * - **name/github**\n - **description**\n - **Latest Pypi version**\n - **Test passing**\n - **apptainers**\n * - `sequana_pipetools <https://github.com/sequana/sequana_pipetools>`_\n - Create and Manage Sequana pipeline\n - .. image:: https://badge.fury.io/py/sequana-pipetools.svg\n :target: https://pypi.python.org/pypi/sequana_pipetools\n - .. image:: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml\n - Not required\n * - `sequana-wrappers <https://github.com/sequana/sequana-wrappers>`_\n - Set of wrappers to build pipelines\n - Not on pypi\n - .. image:: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml\n - Not required\n * - `demultiplex <https://github.com/sequana/demultiplex>`_\n - Demultiplex your raw data\n - .. image:: https://badge.fury.io/py/sequana-demultiplex.svg\n :target: https://pypi.python.org/pypi/sequana-demultiplex\n - .. image:: https://github.com/sequana/demultiplex/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/demultiplex/actions/workflows/main.yml\n - License restriction\n * - `denovo <https://github.com/sequana/denovo>`_\n - denovo sequencing data\n - .. image:: https://badge.fury.io/py/sequana-denovo.svg\n :target: https://pypi.python.org/pypi/sequana-denovo\n - .. image:: https://github.com/sequana/denovo/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/denovo/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/denovo/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/denovo/actions/workflows/apptainer.yml\n * - `fastqc <https://github.com/sequana/fastqc>`_\n - Get Sequencing Quality control\n - .. image:: https://badge.fury.io/py/sequana-fastqc.svg\n :target: https://pypi.python.org/pypi/sequana-fastqc\n - .. image:: https://github.com/sequana/fastqc/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/fastqc/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/fastqc/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/fastqc/actions/workflows/apptainer.yml\n * - `LORA <https://github.com/sequana/lora>`_\n - Map sequences on target genome\n - .. image:: https://badge.fury.io/py/sequana-lora.svg\n :target: https://pypi.python.org/pypi/sequana-lora\n - .. image:: https://github.com/sequana/lora/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/lora/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/lora/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/lora/actions/workflows/apptainer.yml\n * - `mapper <https://github.com/sequana/mapper>`_\n - Map sequences on target genome\n - .. image:: https://badge.fury.io/py/sequana-mapper.svg\n :target: https://pypi.python.org/pypi/sequana-mapper\n - .. image:: https://github.com/sequana/mapper/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/mapper/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/mapper/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/mapper/actions/workflows/apptainer.yml\n * - `nanomerge <https://github.com/sequana/nanomerge>`_\n - Merge barcoded (or unbarcoded) nanopore fastq and reporting\n - .. image:: https://badge.fury.io/py/sequana-nanomerge.svg\n :target: https://pypi.python.org/pypi/sequana-nanomerge\n - .. image:: https://github.com/sequana/nanomerge/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/nanomerge/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/nanomerge/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/nanomerge/actions/workflows/apptainer.yml\n * - `pacbio_qc <https://github.com/sequana/pacbio_qc>`_\n - Pacbio quality control\n - .. image:: https://badge.fury.io/py/sequana-pacbio-qc.svg\n :target: https://pypi.python.org/pypi/sequana-pacbio-qc\n - .. image:: https://github.com/sequana/pacbio_qc/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/pacbio_qc/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/pacbio_qc/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/pacbio_qc/actions/workflows/apptainer.yml\n * - `ribofinder <https://github.com/sequana/ribofinder>`_\n - Find ribosomal content\n - .. image:: https://badge.fury.io/py/sequana-ribofinder.svg\n :target: https://pypi.python.org/pypi/sequana-ribofinder\n - .. image:: https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/ribofinder/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/ribofinder/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/ribofinder/actions/workflows/apptainer.yml\n * - `rnaseq <https://github.com/sequana/rnaseq>`_\n - RNA-seq analysis\n - .. image:: https://badge.fury.io/py/sequana-rnaseq.svg\n :target: https://pypi.python.org/pypi/sequana-rnaseq\n - .. image:: https://github.com/sequana/rnaseq/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/rnaseq/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/rnaseq/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/rnaseq/actions/workflows/apptainer.yml\n * - `variant_calling <https://github.com/sequana/variant_calling>`_\n - Variant Calling\n - .. image:: https://badge.fury.io/py/sequana-variant-calling.svg\n :target: https://pypi.python.org/pypi/sequana-variant-calling\n - .. image:: https://github.com/sequana/variant_calling/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/variant_calling/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/variant_calling/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/variant_calling/actions/workflows/apptainer.yml\n * - `multicov <https://github.com/sequana/multicov>`_\n - Coverage (mapping)\n - .. image:: https://badge.fury.io/py/sequana-multicov.svg\n :target: https://pypi.python.org/pypi/sequana-multicov\n - .. image:: https://github.com/sequana/multicov/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/multicov/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/coverage/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/coverage/actions/workflows/apptainer.yml\n * - `laa <https://github.com/sequana/laa>`_\n - Long read Amplicon Analysis\n - .. image:: https://badge.fury.io/py/sequana-laa.svg\n :target: https://pypi.python.org/pypi/sequana-laa\n - .. image:: https://github.com/sequana/laa/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/laa/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/laa/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/laa/actions/workflows/apptainer.yml\n * - `revcomp <https://github.com/sequana/revcomp>`_\n - reverse complement of sequence data\n - .. image:: https://badge.fury.io/py/sequana-revcomp.svg\n :target: https://pypi.python.org/pypi/sequana-revcomp\n - .. image:: https://github.com/sequana/revcomp/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/revcomp/actions/workflows/main.yml\n - .. image:: https://github.com/sequana/revcomp/actions/workflows/apptainer.yml/badge.svg\n :target: https://github.com/sequana/revcomp/actions/workflows/apptainer.yml\n * - `downsampling <https://github.com/sequana/downsampling>`_\n - downsample sequencing data\n - .. image:: https://badge.fury.io/py/sequana-downsampling.svg\n :target: https://pypi.python.org/pypi/sequana-downsampling\n - .. image:: https://github.com/sequana/downsampling/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/downsampling/actions/workflows/main.yml\n - Not required\n * - `depletion <https://github.com/sequana/depletion>`_\n - remove/select reads mapping a reference\n - .. image:: https://badge.fury.io/py/sequana-downsampling.svg\n :target: https://pypi.python.org/pypi/sequana-depletion\n - .. image:: https://github.com/sequana/depletion/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/depletion/actions/workflows/main.yml\n -\n\n\n\n\n\n.. list-table:: Pipelines not yet released\n :widths: 20 40 20 20\n :header-rows: 1\n\n * - **name/github**\n - **description**\n - **Latest Pypi version**\n - **Test passing**\n * - `trf <https://github.com/sequana/trf>`_\n - Find repeats\n - .. image:: https://badge.fury.io/py/sequana-trf.svg\n :target: https://pypi.python.org/pypi/sequana-trf\n - .. image:: https://github.com/sequana/trf/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/trf/actions/workflows/main.yml\n * - `multitax <https://github.com/sequana/multitax>`_\n - Taxonomy analysis\n - .. image:: https://badge.fury.io/py/sequana-multitax.svg\n :target: https://pypi.python.org/pypi/sequana-multitax\n - .. image:: https://github.com/sequana/multitax/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/multitax/actions/workflows/main.yml\n\n**Please see the** `documentation <http://sequana.readthedocs.org>`_ for an\nup-to-date status and documentation.\n\n\nContributors\n============\n\nMaintaining Sequana would not have been possible without users and contributors.\nEach contribution has been an encouragement to pursue this project. Thanks to all:\n\n.. image:: https://contrib.rocks/image?repo=sequana/sequana\n :target: https://github.com/sequana/sequana/graphs/contributors\n\n\n\nChangelog\n~~~~~~~~~\n\n========= ==========================================================================\nVersion Description\n========= ==========================================================================\n0.17.0 * viz submodules: remove easydev and cleanup scipy imports\n * remove the substractor utility (use sequana_depletion pipeline instead)\n * remove get_max_gc_correlation function from bedtools. not used.\n * Major change in VCF reader (freebayes). Got rid of freebayes_bcf_filter\n redundant with freebayes_vcf_filter; replace scipy fisher test with own\n implementation. Remove useless VCF code.\n * Fixes rnadiff HTML report\n * speedup kegg enrichment using multiprocess\n * Allow sequana_taxonomy to download toydb and viruses_masking DBs from \n zenodo\n0.16.9 * Major fix on PCA and add batch effect plots in RNAdiff analysis\n * count matrix and DESeq2 output files' headers fixed with missing index\n (no impact on analysis but only for those willing to use the CSV files\n in excel)\n * Taxonomy revisited to save taxonomy.dat in gzipped CSV format.\n0.16.8 * update IEM for more testing\n * better handling of error in RNADiff\n * Add new methods for ribodesigner\n0.16.7 * Stable release (fix doc), deprecated.\n0.16.6 * Refactor IEM to make it more robust with more tests.\n0.16.5 * refactor to use pyproject instead of setuptools\n * remove pkg_resources (future deprecation)\n * remove unused requirements (cookiecutter, adjusttext, docutuils, mock,\n psutil, pykwalify)\n * cleanup resources (e.g. moving canvas/bar.py into viz)\n0.16.4 * hot fixes on RNAdiff reports and enrichments\n0.16.3 * Remove all rules (see https://github.com/sequana/sequana-wrappers)\n instead\n * add precommit for developers and applied to all modules and doc\n * Fix wrong import for sequana standalone (regression)\n0.16.2 * save coverage PNG image (regression)\n * Update taxonomy/coverage standalone (regression) and more tests\n0.16.1 * hotfix missing module\n0.16.0 * add mpileup module\n * homogenization enrichment + fixup rnadiff\n * Complete refactoring of sequana coverage module.\n Allow sequana_coverage to handle small eukaryotes in a more memory\n efficient way.\n * use click for the sequana_taxonomy and sequana_coverage and\n sequana rnadiff command\n * Small fixup on homer, idr and phantom modules (for chipseq pipeline)\n0.15.4 * add plot for rnaseq/rnadiff\n0.15.3 * add sequana.viz.plotly module. use tqdm in bamtools module\n * KEGG API changed. We update sequana to use headless server and keep\n the feature of annotated and colored pathway.\n * Various improvements on KEGG enrichment including saving pathways,\n addition --comparison option in sequana sub-command, plotly plots, etc\n0.15.2 * ribodesigner can now accept an input fasta with no GFF assuming the\n fasta already contains the rRNA sequences\n * Fix IEM module when dealing with double indexing\n * Fix anchors in HTML reports (rnadiff module)\n * refactorise compare module to take several rnadiff results as input\n * enrichment improvements (export KEGG and GO as csv files\n0.15.1 * Fix creation of images directory in modules report\n * add missing test related to gff\n * Fix #804\n0.15.0 * add logo in reports\n * RNADiff reports can now use shrinkage or not (optional)\n * remove useless rules now in sequana-wrappers\n * update main README to add LORA in list of pipelines\n * Log2FC values are now **shrinked log2FC** values in volcano plot\n and report table. \"NotShrinked\" columns for Log2FC and Log2FCSE\n prior shrinkage are displayed in report table.\n0.14.6 * add fasta_and_gff_annotation module to correct fasta and gff given a\n vcf file.\n * add macs3 module to read output of macs3 peak detector.\n * add idr module to read results of idr analysis\n * add phantom module to compute phantom peaks\n * add homer module to read annotation files from annotatePeaks\n0.14.5 * move start_pipeline standalone in\n https://github.com/sequana/sequana_pipetools\n * update snpeff module to allows build command to have options\n0.14.4 * hotfix bug on kegg colorised pathways\n * Fix the hover_name in rnadiff volcano plot to include the\n index/attribute.\n * pin snakemake to be >=7.16\n0.14.3 * new fisher metric in variant calling\n * ability to use several feature in rnaseq/rnadiff\n * pin several libaries due to regression during installs\n0.14.2 * Update ribodesigner\n0.14.1 * Kegg enrichment: add gene list 'all' and fix incomplete annotation case\n * New uniprot module for GO term enrichment and enrichment\n refactorisation (transparent for users)\n0.14.0 * pinned click>=8.1.0 due to API change (autocomplete)\n * moved tests around to decrease packaging from 16 to 4Mb\n * ribodesigner: new plots, clustering and notebook\n0.13.X * Remove useless standalones or moved to main **sequana** command\n * Move sequana_lane_merging into a subcommand (sequana lane_merging)\n * General cleanup of documentation, test and links to pipelines\n * add new ribodesigner subcommand\n0.12.X * remove some rules now in https://github.com/sequana/sequana-wrappers\n * refactorisation of VCF tools/modules to use vcfpy instead of pyVCF\n * complete change log before 0.12.4 in the github /doc/Changelog.txt\n========= ==========================================================================\n\n",
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