sequana-revcomp 0.9.0

reverse complement a set of FastQ files

This is is the revcomp pipeline from the Sequana projet

Overview:

revert and complement input Fast files

Input:

A set of FastQ files (paired or single-end) compressed or not

Output:

A set of reverse completed 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

Authors:

Thomas Cokelaer

This is is the fastqc pipeline from the Sequana projet

Overview:

Runs fastqc and multiqc on a set of Sequencing data to produce control quality reports

Input:

A set of FastQ files (paired or single-end) compressed or not

Output:

an HTML file summary.html (individual fastqc reports, mutli-samples report)

Status:

production

Wiki:

https://github.com/sequana/fastqc/wiki

Documentation:

This README file, the Wiki from the github repository (link above) and https://sequana.readthedocs.io

Citation:

Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://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 --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
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.

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
0.8.4	implemented –from-project option
0.8.3	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