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 a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the UserGuide provided on Jellyfish's home page 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 an easier to compiled packaged tar ball of the source code, download a release from home page of Jellyfish at the University of Maryland or from the github release.
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 of Jellyfish, using the shared library of Jellyfish in C++ or with scripting languages. The examples are not compiled by default. Each subdirectory of examples is independent and is compiled with a simple invocation of 'make'.
Bindings to Ruby, Python and Perl are provided. This binding allows to read the output file of Jellyfish directly in a scripting language. Compilation of the bindings is easier from the release tarball: SWIG is not required and in the command lines shown below, remove the --enable-swig switch. Only the development files of the scripting languages are required.
Compilation of the bindings from the git tree requires SWIG version 3, and the development files of the scripting languages. To compile all three bindings, configure with:
./configure --enable-swig --enable-ruby-binding --enable-python-binding --enable-perl-bindingNote that the headers of older version of Perl 5 do not compile with recent compilers (g++ > 4.4, clang++) and C++11 mode enable. One may have to specify the path to version 4.4 of gcc by adding, for example, CXX=g++4.4 to the configure commande line.
The binding can installed in a different location than the default (which may require root privileges for example) by passing a path to the --enable switches. Then, for Python, Ruby or Perl to find the binding, an environment variable may need to be adjusted (PYTHONPATH, RUBYLIB and PERL5LIB respectively). For example:
./configure --prefix=$HOME --enable-swig --enable-python-binding=$HOME/lib/python
export PYTHONPATH=$HOME/lib/pythonSee the swig directory for examples on how to use the bindings.