sequana-depletion 0.4.0

A pipeline to deplete reads from a given reference

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

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.