Prinseq

Introduction

Prinseq is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data.

For more information, please check its website: https://biocontainers.pro/tools/prinseq and its home page: http://prinseq.sourceforge.net.

Versions

0.20.4

Commands

prinseq-graphs-noPCA.pl
prinseq-graphs.pl
prinseq-lite.pl

Module

You can load the modules by:

module load biocontainers
module load prinseq

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Prinseq on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=prinseq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers prinseq

prinseq-lite.pl -verbose -fastq  SRR5043021_1.fastq -fastq2 SRR5043021_2.fastq -graph_data test.gd -out_good null -out_bad null
prinseq-graphs.pl -i test.gd -png_all -o test
prinseq-graphs-noPCA.pl -i test.gd -png_all -o test_noPCA