rob-p / Jellyfish

Fork of the jellyfish kmer counter. Here is the description copied from their site: 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 stats" command. See the documentation below for more details.

Installation
============

% ./configure
% make
# As root:
% make install

To install in a custom directory:

% ./configure --prefix=/my/dir
% make
% make install

Then make sure the following environment variables contain the correct
paths:

PATH            -> /my/dir/bin
LD_LIBRARY_PATH -> /my/dir/lib
MANPATH         -> /my/dir/share/man
PKG_CONFIG_PATH -> /my/dir/lib/pkgconfig

Only the PATH environment variables is necessary to run
jellyfish. MANPATH is used by the man command. PKG_CONFIG_PATH and
LD_LIBRARY_PATH are used to compile software against the jellyfish
shared library.

Tests
=====

To run the built-in tests, do:

% make check

All tests should pass and 1 test should be skipped (big.sh). Running
'make check' will use about 50MB of disk space and will use every CPUs
found on the machine. On our test machine with 32 cores, it takes a
few minutes to run.

To tests also on large data set, do:

% make check BIG=1

WARNING: this uses >40GB of disk space and takes 30 minutes to run (20
to create the data, 10 to run jellyfish).

Notes
=====

* Jellyfish has been devellopped and tested on x86-64 GNU/Linux. It
  compiles and runs correctly the tests on MacOS X (Intel) and
  FreeBSD. It should be fairly easy to port on other *NIX platform
  with the gcc compiler, but no guarantee is made. Support for 32-bits
  platform has not been tested.

License
=======

* The Mersenne Twister random generator is copyrighted by Agner Fog
  and distributed under the GPL version 3 or
  higher. http://www.agner.org.

* The Half float implementation is copyrighted by Industrial Light &
  Magic and is distributed under the license described in the
  HalfLICENSE file.

*   This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.