SlackBuilds Repository

15.0 > Academic > trimmomatic (0.39)

Trimmomatic: A flexible read trimming tool for Illumina NGS data

Trimmomatic performs a variety of useful trimming tasks for illumina
paired-end and single ended data.The selection of trimming steps and
their associated parameters are supplied on the command line.

The current trimming steps are:

- ILLUMINACLIP: Cut adapter and other illumina-specific sequences from
the read.
- SLIDINGWINDOW: Perform a sliding window trimming, cutting once the
average quality within the window falls below a threshold.
- LEADING: Cut bases off the start of a read, if below a threshold
- TRAILING: Cut bases off the end of a read, if below a threshold
- CROP: Cut the read to a specified length
- HEADCROP: Cut the specified number of bases from the start of the
- MINLEN: Drop the read if it is below a specified length
- TOPHRED33: Convert quality scores to Phred-33
- TOPHRED64: Convert quality scores to Phred-64

It works with FASTQ (using phred + 33 or phred + 64 quality scores,
depending on the Illumina pipeline used), either uncompressed or
gzipp'ed FASTQ. Use of gzip format is determined based on the .gz

For single-ended data, one input and one output file are specified,
plus the processing steps. For paired-end data, two input files are
specified, and 4 output files, 2 for the 'paired' output where both
reads survived the processing, and 2 for corresponding 'unpaired'
output where a read survived, but the partner read did not.

Bolger, A. M., Lohse, M., & Usadel, B. (2014).
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bioinformatics, btu170.

This requires: zulu-openjdk11

Maintained by: Petar Petrov
Keywords: trimming,illumina
ChangeLog: trimmomatic


Source Downloads: (271ed9dca91132eee0c960e0ae487bcd)

Download SlackBuild:
trimmomatic.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Validated for Slackware 15.0

See our HOWTO for instructions on how to use the contents of this repository.

Access to the repository is available via:
ftp git cgit http rsync

© 2006-2023 Project. All rights reserved.
Slackware® is a registered trademark of Patrick Volkerding
Linux® is a registered trademark of Linus Torvalds