sickle - windowed adaptive trimming tool for FASTQ files using quality

Property Value
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
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_1.33-1_amd64.deb 1.33 amd64 Ubuntu Universe
sickle - - -


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


Type URL
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




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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