sequana-downsampling

This is is the downsampling pipeline from the Sequana project

Overview:: downsample NGS data sets
Input:: a set of FastQ or FASTA files
Output:: a set of downsampled files
Status:: mature
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

You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_downsampling

Usage

sequana_pipelines_downsampling --help
sequana_pipelines_downsampling --input-directory DATAPATHH
sequana_downsampling --downsampling-method random --downsampling-max-entries 100

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

cd downsampling
sh downsampling.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 downsampling.rules -c config.yaml --cores 4 --stats stats.txt

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s):

sequana
pigz

Details

This pipeline runs downsampling in parallel on the input fastq or fasta files (paired or not).

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
0.8.2	add a –run option to execute the pipeline directly
0.8.1	fix input and N in the random selection
0.8.0	First release.

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