Trimmomatic is a tool for various trimming tasks for the Illumina sequencing data. It allows to remove low quality bases
from the sequence end and (potentially more importantly) to also remove remaining adapters etc from the reads.
One should specify trimming parameters via the command line. It looks a bit awkward at a glance but actually quite easy.
It starts via "java -jar SE" (for the single end data) followed by parameters:
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
For example, following code trimming back trailing bases with qualities of under 30 maintaining a read length of at
least 50 bp:
