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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
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
Authors:Thomas Cokelaer


You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_revcomp


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  # for a local run
make clean

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.


This pipelines requires the following executable(s):

  • seqtk


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.


Version Description
  • implemented –from-project option
  • Uses new sequana framework to spee up –help calls
  • –threads option
0.8.2 Fix schema and rule. output files are now saved in the ./rc directory
0.8.1 Improve the –help message
0.8.0 First version from sequana 0.8.0

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