A powerful toolset for genome arithmetic.
C++ C Shell Other
Pull request Compare This branch is 657 commits ahead, 877 commits behind arq5x:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
data
genomes
scripts
src
test
LICENSE
Makefile
README.rst
RELEASE_HISTORY

README.rst

BEDTools

Created by Aaron Quinlan Spring 2009.

Copyright 2009,2010,2011 Aaron Quinlan. All rights reserved.

Stable releases: http://code.google.com/p/bedtools

Repository: https://github.com/arq5x/bedtools

Released under GNU public license version 2 (GPL v2).

Summary

BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in BED, GTF/GFF, VCF and BAM formats.

Manual

See the extensive PDF manual included at: http://code.google.com/p/bedtools/downloads/detail?name=BEDTools-User-Manual.v4.pdf.

This manual covers many common usage examples. There are also examples available at: http://code.google.com/p/bedtools/wiki/Usage http://code.google.com/p/bedtools/wiki/UsageAdvanced

Installation

Git

git clone git://github.com/arq5x/bedtools.git

Download tarball - that big gray button on the upper right.

  1. Unpack the source downloaded tarball.
  2. cd into the expanded folder.
  3. Type "make" and hit enter.
  4. If you encountered no errors, then bedtools should now be in bin/
If not, try to troubleshoot then email me: aaronquinlan at gmail dot com
  1. Run the test suite with: "make test"
  2. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin. Make sure that the directory to which you copy the tools is in your $PATH
  3. Use the tools.