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.