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Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

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pybedtools is a Python wrapper for Aaron Quinlan's BEDtools and extends these "genome algebra" programs by offering feature-level manipulations from with Python. See full online documentation, including installation instructions, at

Created by Ryan Dale 2010. Copyright 2010, 2011, 2012 Ryan Dale, all rights reserved.

pybedtools is released under the GPLv2 license; see LICENSE.txt for more info.


If you use :mod:`pybedtools` in your work, please cite the pybedtools manuscript:

Dale RK, Pedersen BS, and Quinlan AR. 2011. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics 27(24):3423-3424.

And the BEDTools manuscript:

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841–842.
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