trimmomatic_0.35+dfsg-1_all.deb


Advertisement

Description

trimmomatic - flexible read trimming tool for Illumina NGS data

Property Value
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

Package Version Architecture Repository
trimmomatic_0.35+dfsg-1_all.deb 0.35+dfsg all Ubuntu Universe
trimmomatic - - -

Requires

Name Value
default-jre -
libjbzip2-java -

Download

Type URL
Binary Package trimmomatic_0.35+dfsg-1_all.deb
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

Path
/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).

See Also

Package Description
trinity_1.6-2_i386.deb system call fuzz tester
triplane_1.0.8-1_i386.deb side-scrolling dogfighting game
triplea_1.7.0.3+dfsg-1_all.deb Turn based strategy game
tripwire_2.4.2.2-5_i386.deb file and directory integrity checker
tritium_0.3.8-3_all.deb tabbed/tiling window manager
trocla_0.2.3-1_all.deb generate and store passwords and certificates on a central server
troffcvt_1.04-23_i386.deb Converts troff source to HTML, RTF, and plain text
trophy-data_2.0.3-1build1_all.deb data files for trophy
trophy_2.0.3-1build1_i386.deb 2D car racing action game
tropic-gdm-theme_0.2-0ubuntu2_all.deb Tropic look - GDM theme
tropic-look_0.2-0ubuntu2_all.deb Tropic look - metapackage
tropic-session-splashes_0.2-0ubuntu2_all.deb Tropic look - Session splashes
tropic-theme_0.2-0ubuntu2_all.deb Tropic look - GTK and Metacity theme
tropic-wallpapers_0.2-0ubuntu2_all.deb Tropic look - Wallpapers
trovacap-data_0.2.2-1_all.deb tool to find Italian ZIP codes - ZIP codes database
Advertisement
Advertisement