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

0.8.4

  • add missing MANIFEST to include missing requirements.txt

0.8.3

  • comply with new API from sequana_pipetools 0.2.4

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.

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.10.0)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for cokelaer from gravatar.com cokelaer

Credits

Author/Maintainer: thomas cokelaer

License

BSD License (new BSD)

Tags

NGS sequana snakemake fastq downsampling

Classifiers

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