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.
For more information, please check its website: https://biocontainers.pro/tools/prinseq and its home page: http://prinseq.sourceforge.net.
- 0.20.4
- prinseq-graphs-noPCA.pl
- prinseq-graphs.pl
- prinseq-lite.pl
You can load the modules by:
module load biocontainers module load prinseq
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run Prinseq on our clusters:
#!/bin/bash #SBATCH -A myallocation # Allocation name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=prinseq #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge ml biocontainers prinseq prinseq-lite.pl -verbose -fastq SRR5043021_1.fastq -fastq2 SRR5043021_2.fastq -graph_data test.gd -out_good null -out_bad null prinseq-graphs.pl -i test.gd -png_all -o test prinseq-graphs-noPCA.pl -i test.gd -png_all -o test_noPCA