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Source: trimmomatic
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Steffen Moeller <moeller@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
default-jdk | openjdk-7-jdk,
javahelper,
ant,
libjbzip2-java
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/trimmomatic/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/trimmomatic/trunk/
Homepage: http://www.usadellab.org/cms/index.php?page=trimmomatic
Package: trimmomatic
Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends},
libjbzip2-java,
default-jre
Description: 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 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.
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