trimmomatic_0.35+dfsg-1_all.deb


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Description

trimmomatic - flexible read trimming tool for Illumina NGS data

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe i386
Package name: trimmomatic
Package version: 0.35+dfsg
Package release: 1
Package architecture: all
Package type: deb
Installed size: 151 B
Download size: 111.29 KB
Official Mirror: archive.ubuntu.com
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 thes average quality within the window falls below a threshold. * LEADING: Cut bases off the start of a read, if below a threshold quality * TRAILING: Cut bases off the end of a read, if below a threshold quality * CROP: Cut the read to a specified length * HEADCROP: Cut the specified number of bases from the start of the read * MINLENGTH: 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 extension.

Alternatives

    Download

    Source package: trimmomatic

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install trimmomatic deb package:
      # sudo apt-get install trimmomatic

    Files

    • /usr/bin/TrimmomaticPE
    • /usr/bin/TrimmomaticSE
    • /usr/share/doc/trimmomatic/README.Debian
    • /usr/share/doc/trimmomatic/changelog.Debian.gz
    • /usr/share/doc/trimmomatic/copyright
    • /usr/share/doc/trimmomatic/examples/batchTrim
    • /usr/share/java/trimmomatic-0.35.jar
    • /usr/share/java/trimmomatic.jar
    • /usr/share/man/man1/TrimmomaticPE.1.gz
    • /usr/share/man/man1/TrimmomaticSE.1.gz
    • /usr/share/trimmomatic/NexteraPE-PE.fa
    • /usr/share/trimmomatic/TruSeq2-PE.fa
    • /usr/share/trimmomatic/TruSeq2-SE.fa
    • /usr/share/trimmomatic/TruSeq3-PE-2.fa
    • /usr/share/trimmomatic/TruSeq3-PE.fa
    • /usr/share/trimmomatic/TruSeq3-SE.fa

    Changelog

    2015-11-26 - Andreas Tille <tille@debian.org> trimmomatic (0.35+dfsg-1) unstable; urgency=medium * New upstream version * Add example script for processing heaps of sequences

    2015-05-19 - Andreas Tille <tille@debian.org> trimmomatic (0.33+dfsg-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control

    2015-02-27 - Andreas Tille <tille@debian.org> trimmomatic (0.32+dfsg-4) unstable; urgency=medium * Also adjust manpage to make sure users will be properly informed about the adapter location since the package might be useless without this information (so the issue is closely related to bug #779296)

    2015-02-26 - Andreas Tille <tille@debian.org> trimmomatic (0.32+dfsg-3) unstable; urgency=medium * Install adapter files and document their usage in d/README.Debian Closes: #779296

    2014-12-16 - Andreas Tille <tille@debian.org> trimmomatic (0.32+dfsg-2) unstable; urgency=medium * Fix bashism in wrapper script Closes: #772392

    2014-01-13 - Andreas Tille <tille@debian.org> trimmomatic (0.32+dfsg-1) unstable; urgency=low * debian/copyright: Fix contact and copyright * debian/get-orig-source: Trust new uscan to create clean upstream source tarball * debian/control: cme fix dpkg-control

    2013-08-07 - Andreas Tille <tille@debian.org> trimmomatic (0.30+dfsg-1) unstable; urgency=low * New upstream version * debian/copyright: - DEP5 - Add Files-Excluded to document what was removed from original source * debian/watch: handle +dfsg suffix * debian/get-orig-source: use new uscan if available * debian/control: - cme fix dpkg-control - debhelper 9 - use anonscm in Vcs fields - Build-Depends: default-jdk | ... Closes: #718850 [ Olivier Sallou] * Manage java libs with javahelper * Provide upstream missing MANIFEST.MF

    2012-07-25 - Andreas Tille <tille@debian.org> trimmomatic (0.22-1) unstable; urgency=low * Initial release (Closes: #682213).

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