sickle - windowed adaptive trimming tool for FASTQ files using quality

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe i386
Package name: sickle
Package version: 1.33
Package release: 1
Package architecture: i386
Package type: deb
Installed size: 72 B
Download size: 17.88 KB
Official Mirror:
Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end. Incorrectly called bases here 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. 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 drops below the threshold. At that point the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there. However, if the cut point is less than the minimum length threshold, then the read is discarded entirely. Sickle supports four types of quality values: Illumina, Solexa, Phred, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close. Sickle also supports gzipped file inputs.



    Binary package: sickle_1.33-1_i386.deb
    Source package: sickle

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install sickle deb package:
      # sudo apt-get install sickle


    • /usr/bin/sickle
    • /usr/share/doc/sickle/
    • /usr/share/doc/sickle/changelog.Debian.gz
    • /usr/share/doc/sickle/copyright
    • /usr/share/man/man1/sickle.1.gz


    2015-06-23 - Andreas Tille <> sickle (1.33-1) unstable; urgency=medium * Initial upload to Debian (Closes: #789707)

    2014-05-07 - Tim Booth <> sickle (0.94-1biolinux1.1) trusty; urgency=low * Rebuild for Trusty * Pass standard CFLAGS to build

    2013-04-29 - Tim Booth <> sickle (0.94-0precise2) precise; urgency=low * Fix manpage to have more useful info

    2013-04-29 - Tim Booth <> sickle (0.94-0precise1) precise; urgency=low * Initial build for PPA.