BFCounter is a memory efficient program for counting k-mers from sequencing files.

Installation

Just run make to compile.

% make

The default maximum k-mer size supported is 31 (8 bytes of memory per k-mer), to modify this either replace MAX_KMER_SIZE in Makefile with an appropriate number or directly to make with

% make MAX_KMER_SIZE=64

In this case it the maximum k-mer size allowed is 63, and each k-mer will use 16 bytes of memory.

Running

To run the program use

% ./BFCounter

To list available commands

% ./BFCounter count % ./BFCounter dump

will provide more complete help.

Notes

• BFCounter dump will print a text file with each k-mer and the number of occurrances of the k-mer. Only counts of 2 and greater will be printed, there is no limit on the number of occurrances it can handle. For each k-mer only the lexicographically smaller of the k-mer and the reverse complement of the k-mer, will be printed and the counts will be the sum of both values.

• BFCounter was developed on x86-64 GNU/Linux. Porting to other unix-like platforms should be easy, but we haven't done so yet.

• If you run into bugs or problems or have suggestions for future versions please contact me at [email protected]

License

• The hash functions used are from the MurmurHash Library, version 3, released under the MIT License. http://code.google.com/p/smhasher/

• The kseq functions for reading fast(a|q)(.gz) files are copyrighted by Heng Li and released under the MIT License. http://lh3lh3.users.sourceforge.net/kseq.shtml

• The Google sparsehash library is copyrighted by Google and released under a BSD License. http://code.google.com/p/google-sparsehash/

• 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/.