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Jellyfish

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  • Version: 2.1

Jellyfish


Jellyfish mer counter

What is it?

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 quickly 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. See the documentation below for more details.

Jellyfish is distributed as source code under the GPL license . Jellyfish is developed on Linux 64-bit (x86_64). It requires gcc version 4.4 or newer to compiles. It is reported to compile on Linux with the clang compiler version 3.0, MacOS X (Intel 64 bit) with gcc version 4.7 and Microsoft Windows 7 with cygwin and gcc.


Access mode(s):

Command line on saruman.versailles.inra.fr


Creation date: 01 Oct 2014