Jellyfish
Description
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.
License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of jellyfish and load default version of jellyfish as
module avail jellyfish/ # list available modules module load jellyfish # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail jellyfish
and choose explicit version you want to use.
Documentation
Documentation is available in JellyfishUserGuide.pdf or it's local copy at /software/jellyfish-2.1.3/share/doc/JellyfishUserGuide.pdf.