Difference between revisions of "Applications/Prinseq-lite"

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(Created page with "__TOC__ ==Application Details== * Description: PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data. * Version: 0.20.4 * Modules: prinseq-l...")
 
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* Version: 0.20.4
 
* Version: 0.20.4
 
* Modules: prinseq-lite/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]
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* 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]
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===Introduction===
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 +
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 Examples==
 +
 
Usage information can be found at [http://prinseq.sourceforge.net/manual.html http://prinseq.sourceforge.net/manual.html]
 
Usage information can be found at [http://prinseq.sourceforge.net/manual.html http://prinseq.sourceforge.net/manual.html]
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 +
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)
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 +
===Interactive Session===
  
 
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
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 +
[username@login01 ~]$ interactive
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salloc: Granted job allocation 3619683
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Job ID 3619683 connecting to c025, please wait...
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c025.vc-main
  
 
[username@login01 ~]$ module add prinseq-lite/0.20.4
 
[username@login01 ~]$ module add prinseq-lite/0.20.4
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[username@login01 ~]$ prinseq-lite.pl <input/output options>
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</pre>
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* Use  prinseq-lite.pl -help for help on the options here
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===Batch Script===
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<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
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 +
#!/bin/bash
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#SBATCH -J prin-seq
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#SBATCH -N 1
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#SBATCH --ntasks-per-node 1
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#SBATCH -D /home/username/
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#SBATCH -o %N.%j.%a.out
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#SBATCH -e %N.%j.%a.err
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#SBATCH -p compute
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module add prinseq-lite/0.20.4
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prinseq-lite.pl <input/output options>
  
 
</pre>
 
</pre>
  
==Further Information==
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 +
==Next Steps==
  
 
* [http://prinseq.sourceforge.net/index.html http://prinseq.sourceforge.net/index.html]
 
* [http://prinseq.sourceforge.net/index.html http://prinseq.sourceforge.net/index.html]
  
{|
+
{{Modulepagenav}}
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 
|style="width:95%; border-width: 0" |
 
* [[Main_Page|Home]]
 
* [[Applications|Application support]]
 
* [[General|General]]
 
* [[Training|Training]]
 
* [[Programming|Programming support]]
 
|-
 
|}
 

Latest revision as of 16:45, 16 November 2022

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





Modules | Main Page | Further Topics