sequana-depletion

JOSS (journal of open source software) DOI

https://github.com/sequana/depletion/actions/workflows/main.yml/badge.svg

This is is the depletion pipeline from the Sequana project

Overview:: select or deplete reads from input FastQ files given a reference
Input:: Fastq Files
Output:: Fastq Files
Status:: production
Citation:: 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

Installation

Install this package as follows:

pip install sequana_depletion

it requires https://sequana.readthedocs.io and https://bioconvert.readthedocs.io for the bam to fastq conversion

Usage

sequana_depletion --help
sequana_depletion --input-directory DATAPATH --reference hg38.fa --mode depletion
sequana_depletion --input-directory DATAPATH --reference covid.fa --mode selection

This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:

cd depletion
sh depletion.sh  # for a local run

This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:

snakemake -s depletion.rules -c config.yaml --cores 4 --stats stats.txt

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s):

bwa
samtools
pigz

https://raw.githubusercontent.com/sequana/depletion/main/sequana_pipelines/depletion/dag.svg

Details

This pipeline runs depletion in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced.

Rules and configuration details

Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.

Changelog

Version	Description
0.4.0	add HTML summary report with per-sample statistics (total reads, selected/depleted reads and percentage) fix samtools flags for all mode/layout combinations (selection+paired, selection+single, depletion+paired, depletion+single) fix single-end crash in depletion_selection shell migrate bwa rules to manager.get_shell(); remove sam2bam rule output files moved to per-sample SAMPLE/cleaned/ directories add rulegraph rule; workflow SVG embedded in report update tools.txt
0.3.0	use click and new sequana_pipetools. convert to pyproject
0.2.0	handle paired/unpaired data refactorise to use containers/apptainers
0.1.0	First release.

Metadata

Release files for sequana-depletion 0.4.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for sequana-depletion 0.4.0
File	Size	Uploaded
sequana_depletion-0.4.0.tar.gz	8.0 kB	Apr 1, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for sequana-depletion 0.4.0
File	Interpreter	ABI	Platform	Reset
sequana_depletion-0.4.0-py3-none-any.whl 10.7 kB Apr 1, 2026	Python 3	none	any	Details

Total release size: 18.7 kB

Release files / sequana_depletion-0.4.0.tar.gz

Download URL	sequana_depletion-0.4.0.tar.gz
Size	8.0 kB
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Uploaded via	`poetry/2.0.1 CPython/3.10.14 Linux/6.14.5-100.fc40.x86_64`

Release files / sequana_depletion-0.4.0-py3-none-any.whl

Download URL	sequana_depletion-0.4.0-py3-none-any.whl
Size	10.7 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`afa22171b682f4cf687376e85e2880dd4fce161277fa70e7145bae77e8f6eb06`
BLAKE2b-256 checksum How to use checksums	`dc3a0dd0b76db668ba94a5cadbc5c8b642cd19a523760b7be034c6c32a09f9c4`
Upload date	Apr 1, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`poetry/2.0.1 CPython/3.10.14 Linux/6.14.5-100.fc40.x86_64`