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.. samtools documentation master file, created by
sphinx-quickstart on Wed Aug 12 14:43:42 2009.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
pysam: samtools interface for python
====================================
:Author: Andreas Heger, Tildon Grant Belgrad, Martin Goodson, Leo Goodstad, Kevin Jacobs
:Date: |today|
:Version: |version|
The *SAM/BAM* format is a way to store efficiently large numbers of alignments
[Li2009]_, such as those routinely are created by next-generation sequencing
methods.
This module provides a low-level wrapper around the samtools_ C-API using `cython`_
and a high-level API for convenient access to the data in *SAM/BAM* formatted files.
Also included is an interface to the tabix_ C-API for reading compressed and
indexed tabular data.
The current version wraps *samtools-0.1.18* and *tabix-0.2.6*.
Contents
--------
.. toctree::
:maxdepth: 2
api.rst
usage.rst
tabix.rst
faq.rst
glossary.rst
developer.rst
release.rst
Indices and tables
------------------
Contents:
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
References
----------
.. [Li2009] The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup.
Bioinformatics. 2009 Aug 15;25(16):2078-9. Epub 2009 Jun 8.
`PMID: 19505943 <http://www.ncbi.nlm.nih.gov/pubmed/19505943?dopt=Abstract>`_
.. seealso::
The samtools homepage
http://samtools.sourceforge.net
The cython C-extensions for python
http://cython.org/
The python language
http://www.python.org
.. _samtools: http://samtools.sourceforge.net
.. _tabix: http://samtools.sourceforge.net/tabix.shtml
.. _cython: http://cython.org/
.. _python: http://www.python.org
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