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A pipeline to deplete reads from a given reference

Project description JOSS (journal of open source software) DOI

This is is the depletion pipeline from the Sequana project


select or deplete reads from input FastQ files given a reference


Fastq Files


Fastq Files




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


Install this package as follows:

pip install sequana_depletion

it requires and for the bam to fastq conversion


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  # 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.


This pipelines requires the following executable(s):

  • bwa

  • samtools

  • bamtools

#.. image::


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.





  • use click and new sequana_pipetools. convert to pyproject


  • handle paired/unpaired data

  • refactorise to use containers/apptainers


First release.

Project details

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