academic/trimmomatic: Added (Trimming Tool).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 38 insertions, 0 deletions

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+Trimmomatic: A 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 the
+  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
+- MINLEN: 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.
+
+For single-ended data, one input and one output file are specified,
+plus the processing steps. For paired-end data, two input files are
+specified, and 4 output files, 2 for the 'paired' output where both
+reads survived the processing, and 2 for corresponding 'unpaired'
+output where a read survived, but the partner read did not.
+
+Citations
+Bolger, A. M., Lohse, M., & Usadel, B. (2014).
+Trimmomatic: A flexible trimmer for Illumina Sequence Data.
+Bioinformatics, btu170.