Trimmomatic

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.