View source for Applications/Prinseq-lite

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==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 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===

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[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>
</pre>

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

===Batch Script===

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

#!/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>

</pre>


==Next Steps==

* [http://prinseq.sourceforge.net/index.html http://prinseq.sourceforge.net/index.html]

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