Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3′-end of reads and also determines when the quality is sufficiently high enough to trim the 5′-end of reads. It will also discard reads based upon the length threshold.
CyVerse UK provides two sickle applications:
one to be used for single reads
one to be used for paired end reads (both in separate files or in a single interleaved file)
