From the GitHub page:

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)

See the github project for more details.

  • Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files
    (Version 1.33) [Software]. Available at
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