jellyfish - count k-mers in DNA sequences

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 parallelism. 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.



    Source package: jellyfish

    Install Howto

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


    • /usr/bin/jellyfish
    • /usr/share/doc-base/jellyfish
    • /usr/share/doc/jellyfish/README.test
    • /usr/share/doc/jellyfish/changelog.Debian.gz
    • /usr/share/doc/jellyfish/changelog.gz
    • /usr/share/doc/jellyfish/copyright
    • /usr/share/doc/jellyfish/jellyfish.pdf.gz
    • /usr/share/doc/jellyfish/run-unit-test
    • /usr/share/man/man1/jellyfish.1.gz


    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.