PrinSeq Lite v0.20.4

PrinSeq is a bioinformatics tool to PRe-process and show INformation of SEQuence data.

Accessing the software

To load the module:

$ module load apps/prinseq/v0.20.4

An example command to include in your job script:

     -fastq input_fastq_file \
     -out_format 3 \
     -no_qual_header \
     -min_len 30 \
     -min_qual_mean 20 \
     -ns_max_p 60 \
     -trim_tail_right 5 \
     -trim_tail_left 5 \
     -trim_qual_step 1 \
     -trim_ns_right 5 \
     -trim_ns_left 5 \
     -trim_qual_right 20 \
     -trim_qual_left 20 \
     -trim_qual_type mean \
     -trim_qual_rule lt \
     -trim_qual_window 5 \
     -out_bad null

Noting the use of the line continuation symbol \.

Command-line options can be viewed with the command:

perl $PRINSEQ_ROOT/ -h

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the PrinSeq website for more information regarding this application.

Last modified: 7 December 2017