Source: trimmomatic Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Steffen Moeller Section: science Priority: optional Build-Depends: debhelper-compat (= 13), default-jdk | openjdk-7-jdk, javahelper, ant, libjbzip2-java Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/trimmomatic Vcs-Git: https://salsa.debian.org/med-team/trimmomatic.git Homepage: http://www.usadellab.org/cms/index.php?page=trimmomatic Rules-Requires-Root: no 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.