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Bug#682213: ITP: trimmomatic -- flexible read trimming tool for Illumina NGS data

Package: wnpp
Severity: wishlist
Owner: Steffen Moeller <steffen_moeller@gmx.de>

* Package name    : trimmomatic
  Version         : 0.22
* URL             : http://www.usadellab.org/cms/index.php?page=trimmomatic
* License         : GPL-3+
  Programming Lang: Java
  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

Packaging is mostly done, inspectable at the typical DebianMed location, i.e.
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/trimmomatic/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/trimmomatic/trunk/

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