sickle - windowed adaptive trimming tool for FASTQ files using quality

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main i386
Package filename sickle_1.33+git20150314.f3d6ae3-1_i386.deb
Package name sickle
Package version 1.33+git20150314.f3d6ae3
Package release 1
Package architecture i386
Package type deb
Category science
License -
Maintainer Debian Med Packaging Team <>
Download size 18.79 KB
Installed size 55.00 KB
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
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.


Package Version Architecture Repository
sickle_1.33+git20150314.f3d6ae3-1_amd64.deb 1.33+git20150314.f3d6ae3 amd64 Debian Main
sickle - - -


Name Value
libc6 >= 2.4
zlib1g >= 1:1.1.4


Type URL
Binary Package sickle_1.33+git20150314.f3d6ae3-1_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




2018-10-24 - Andreas Tille <>
sickle (1.33+git20150314.f3d6ae3-1) unstable; urgency=medium
* Use git mode in watch file to include some interesting commits
after latest release
* debhelper 11
* Point Vcs fields to
* Standards-Version: 4.2.1
* hardening=+all
2017-11-18 - Andreas Tille <>
sickle (1.33-2) unstable; urgency=medium
* Moved packaging from SVN to Git
* debhelper 10
* Standards-Version: 4.1.1
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.

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