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PRINSEQ

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. It is particular designed for 454/Roche data, but can also be used for other types of sequence data.

On our systems, only the main program prinseq-lite.pl is set up for use. Please contact the HPC staff if you require more of PRINSEQ's functionality.

References:

There may be multiple versions of prinseq available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail prinseq

To select a module, type

module load prinseq/[ver]

where [ver] is the version of choice.

Environment variables set:

On Helix

Sample session:

module load prinseq
prinseq-lite.pl -verbose -fastq $PRINSEQ_HOME/example/example1.fastq -ns_max_n 0 -out_good test_no_ns -out_bad test_with_ns
Interactive job on Biowulf

See the Biowulf user guide for interactive jobs.

Batch job on Biowulf

Create a batch input file (e.g. prinseq.sh), which uses the input file 'prinseq.in'. For example:

#!/bin/bash
module load prinseq
prinseq-lite.pl -verbose -fastq $PRINSEQ_HOME/example/example1.fastq -ns_max_n 0 -out_good test_no_ns -out_bad test_with_ns

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=1 prinseq.sh
Swarm of Jobs on Biowulf

Create a swarmfile following the swarm guide using the example commands on this page.

Documentation