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. See the documentation below for more details.
If you use Jellyfish in your research, please cite:
Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 (first published online January 7, 2011) doi:10.1093/bioinformatics/btr011
To get packaged tar ball of the source code, see the home page of Jellyfish at the University of Maryland.
To compile from the git tree, you will need autoconf/automake, make, g++ 4.4 or newer and yaggo. Then compile with:
autoreconf -i
./configure
make
sudo make installIn the examples directory are potentially useful extra programs to query/manipulates output files from Jellyfish. The examples are not compiled by default. Each subdirectory of examples is independent and is compiled with a simple invocation of 'make'.