Skip to main content

reverse complement a set of FastQ files

Project description

This is is the revcomp pipeline from the Sequana projet

Overview:Simply reverse complement a bunch of fastq files
Input:fastq files
Output:their reverse complement counterpart
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

You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_revcomp

Usage

sequana_pipelines_revcomp --help
sequana_pipelines_revcomp --input-directory DATAPATH

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

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

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s):

  • seqtk

Details

This pipeline runs seqtk in parallel on the input fastq files.

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
0.8.1 Improve the –help message
0.8.0 First version from sequana 0.8.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for sequana-revcomp, version 0.8.1
Filename, size File type Python version Upload date Hashes
Filename, size sequana_revcomp-0.8.1.tar.gz (48.3 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page