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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