Commit cd659359 authored by arq5x's avatar arq5x
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update README

parent 75ef783b
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BEDTools
==============================
Created by Aaron Quinlan Spring 2009.
Copyright 2009,2010,2011 Aaron Quinlan. All rights reserved.
Note
-------
Stable release for bedtools were formerly archived on Google Code. Unfortunately, Google Code
is shutting down so henceforth, all source code and stable releases will be maintained via this
Github repository.
Stable releases: http://code.google.com/p/bedtools
Summary
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Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
Repository: https://github.com/arq5x/bedtools
While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Released under GNU public license version 2 (GPL v2).
Details
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Created out of urgency by Aaron Quinlan Spring 2009.
Maintained by the Quinlan Laboratory at the University of Virginia.
Lead developers: Aaron Quinlan, Neil Kindlon
Significant contributions: Assaf Gordon, Royden Clark, John Marshall, Brent Pedersen, Ryan Dale
Repository: https://github.com/arq5x/bedtools2
Stable releases: https://github.com/arq5x/bedtools2/releases
Documentation: bedtools.readthedocs.org
License: Released under GNU public license version 2 (GPL v2).
Summary
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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
5. Run the test suite with: "make test"
6. 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
7. Use the tools.
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