sequana-depletion 0.3.0

Description:

sequanadepletion 0.3.0

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
bamtools

#.. image:: https://raw.githubusercontent.com/sequana/depletion/master/sequana_pipelines/depletion/dag.png


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



0.3.0

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.