Sickle is a windowed adaptive trimming tool for FASTQ file using quality.

Most modern sequencing technologies produce reads that have deteriorating quality towards the 3′-end and some towards the 5′-end as well. Incorrectly called bases in both regions negatively impact assembles, mapping, and downstream bioinformatics analyses.

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. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window rises above the threshold, at which point the algorithm determines where within the window the rise occurs and cuts the read and quality there for the 5′-end cut. Then when the average quality in the window drops below the threshold, the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there for the 3′-end cut. However, if the length of the remaining sequence is less than the minimum length threshold, then the read is discarded entirely.




Usage on Bridges


To see what other modules are needed, what commands are available and how to get additional help type

module help sickle

To see what versions of Sickle are available type

module avail sickle

To use Sickle, include a command like this in your batch script or interactive session to load the Sickle module:

module load sickle

Be sure you also load any other modules needed, as listed by the module help sickle command.