Difference between revisions of "Applications/Prinseq-lite"
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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] | ||
| − | Can be used with the | + | 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=== | ===Interactive Session=== | ||
| Line 32: | Line 32: | ||
[username@login01 ~]$ module add prinseq-lite/0.20.4 | [username@login01 ~]$ module add prinseq-lite/0.20.4 | ||
| − | [username@login01 ~]$ | + | [username@login01 ~]$ prinseq-lite.pl <input/output options> |
</pre> | </pre> | ||
* Use prinseq-lite.pl -help for help on the options here | * 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== | ==Next Steps== | ||
Latest revision as of 16:45, 16 November 2022
Contents
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>