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.