jellyfish - count k-mers in DNA sequences

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main amd64
Package name jellyfish
Package version 2.1.4
Package release 1
Package architecture amd64
Package type deb
Installed size 599 B
Download size 338.87 KB
Official Mirror
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.


Package Version Architecture Repository
jellyfish - - -


Name Value
libc6 >= 2.14
libgcc1 >= 1:4.1.1
libjellyfish-2.0-2 = 2.1.4-1
libstdc++6 >= 4.9


Type URL
Binary Package jellyfish_2.1.4-1_amd64.deb
Source Package jellyfish

Install Howto

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




2014-10-09 - Andreas Tille <>
jellyfish (2.1.4-1) unstable; urgency=medium
* New upstream version
* d/watch: point to new location on Github
* cme fix dpkg-control
* new upstream version needs autoreconf
* New Build-Depends: yaggo, pkg-config, bc, time, procps
* debian/rules: Make sure package builds twice in a row
* d/copyright:
- Adapted to file locations in new upstream version
- Additional copyright paragraph for included libjsoncpp
- Additional copyright paragraph for unit tests
* checking whether it is possible to use Debian packaged libjsoncpp
failed - add lintian override to use internal one
* Split libjellyfish and libjellyfish-dev packages up from single
package, add jellyfish-examples package containing test suite
* Add autopkgtest
* Fix FTBFS with clang (thanks for the patch to Martin Steghöfer)
Closes: #749136
2014-03-21 - Andreas Tille <>
jellyfish (1.1.11-1) unstable; urgency=medium
* New upstream version
* Move debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
2013-06-05 - Andreas Tille <>
jellyfish (1.1.10-1) unstable; urgency=low
* New upstream version
Closes: #701423
* debian/{rules,install}: Make sure dynamic library will be installed
* debian/control:
- Removed DM-Upload-Allowed
- Standards-Version: 3.9.4 (no changes needed)
- Build-Depends autotools-dev
- canonical VCS URLs
* debian/lintian-overrides: Upstream decided to use a dynamic library
without really intending to make this a development package
* debian/doc-base: docbase control file
* debian/patches/man: refreshed + DEP3 description
2012-05-21 - Andreas Tille <>
jellyfish (1.1.5-1) unstable; urgency=low
* New upstream version fixing the FTBFS with gcc-4.7 bug
Closes: #667214
* debian/patches/fix-unused-but-set-variable.patch: Removed
because applied upstream
2012-03-31 - Andreas Tille <>
jellyfish (1.1.4-1) unstable; urgency=low
* New upstream version
* debian/patches/ptrdiff_t: Removed because applied upstream
* debian/patches/cmdline: Removed because upstream code was changed
in a way that it becomes superfluous
* debian/patches/fix-unused-but-set-variable.patch: Due to the use
of hardening flags warnings about unused-but-set-variable becomes
an error - start working on a patch
* debian/source/local-options: Add dpkg-source local-options hints
* debian/control:
- Standards-Version: 3.9.3 (no changes needed)
- Move citation from long desciption to debian/upstream
- debhelper (>= 9)
* debian/upstream: Use the agreed way to specify citations
* debian/copyright: DEP5 verified using
cme fix dpkg-copyright
* debian/compat: 9
2011-10-10 - Shaun Jackman <>
jellyfish (1.1.2-1) unstable; urgency=low
* Initial release. Closes: #644925.

See Also

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