/bfgraph

No description, website, or topics provided.
  1. C++ 94.2%
  2. C 2.0%
  3. Python 1.8%
  4. Makefile 0.8%
  5. CMake 0.5%
  6. Shell 0.4%
  7. Perl 0.3%
C++ C Python Makefile CMake Shell Perl

Clone with HTTPS

Use Git or checkout with SVN using the web URL.

Download ZIP
Find file
Switch branches/tags
Nothing to show
Latest commit da3ff88 May 2, 2016 @pmelsted minor fixes
Permalink
Failed to load latest commit information.
docs More editing Aug 15, 2012
example minor fixes May 2, 2016
old More cleanup Feb 3, 2015
src Code reorg May 2, 2016
tests Cleanup Feb 3, 2015
.gitignore Switching to contigmapper, still not done May 2, 2013
CMakeLists.txt Update readme May 2, 2016
LICENSE Listed all options, and wrote out documentation. Sep 22, 2011
README.md Update readme May 2, 2016
TODO More cleanup Feb 3, 2015
astyle.txt Astyle fixes Feb 10, 2015

README.md

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

Installation

Compilation requires cmake 2.8.12. To build type

% mkdir build % cd build % cmake .. % 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 CMakeLists.txt with an appropriate number

% % set( MAX_KMER_SIZE "64")

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

Running

To run the program use

% ./BFGraph

To list available commands

% ./BFGraph filter % ./BFGraph contigs

will provide more complete help.

Documentation

See docs/BFGDocumentation.pdf You can recompile the documentation by running make inside the directory docs.

Example of usage

The directory example contains two small read files. See the file 'example.sh' to see how to run the program on these files.

Notes

  • BFGraph 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 pmelsted@gmail.com or file an issue

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

  • 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/.