Applications/Prinseq-lite

Application Details

• Description: PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
• Version: 0.20.4
• Modules: prinseq-lite/0.20.4
• Citing: If you use PRINSEQ, please cite Schmieder R and Edwards R: Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011, 27:863-864. [PMID: 21278185]

Introduction

PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data. It generates summary statistics of your sequences in graphical and tabular format. It is easily configurable and provides a user-friendly interface.

Usage Examples

Usage information can be found at http://prinseq.sourceforge.net/manual.html

Can be used with the following file formats:

• FASTA file with sequence data
• QUAL file with quality scores (if available)
• FASTQ file (as alternative format)

Interactive Session

[username@login01 ~]$ interactive
salloc: Granted job allocation 3619683
Job ID 3619683 connecting to c025, please wait...
c025.vc-main

[username@login01 ~]$ module add prinseq-lite/0.20.4
[username@login01 ~]$ prinseq-lite.pl <input/output options>

• Use prinseq-lite.pl -help for help on the options here

Batch Script

#!/bin/bash
#SBATCH -J prin-seq
#SBATCH -N 1
#SBATCH --ntasks-per-node 1
#SBATCH -D /home/username/
#SBATCH -o %N.%j.%a.out
#SBATCH -e %N.%j.%a.err
#SBATCH -p compute

module add prinseq-lite/0.20.4
prinseq-lite.pl <input/output options>

Next Steps

• http://prinseq.sourceforge.net/index.html

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