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=====
Pysam
=====
|build-status| |docs|
Pysam is a python module for reading and manipulating files in the
SAM/BAM format. The SAM/BAM format is a way to store efficiently large
numbers of alignments (`Li 2009`_), such as those routinely created by
next-generation sequencing methods.
Pysam is a lightweight wrapper of the samtools_ C-API. Pysam also
includes an interface for tabix_.
The latest version is available through `pypi
<https://pypi.python.org/pypi/pysam>`_. To install, simply type::
pip install pysam
If you are using the conda packaging manager (e.g. miniconda or anaconda),
you can install pysam from the `bioconda channel <https://bioconda.github.io/>`_:
conda config --add channels r
conda config --add channels bioconda
conda install pysam
Pysam documentation is available through https://readthedocs.org/ from
`here <http://pysam.readthedocs.org/en/latest/>`_
Questions and comments are very welcome and should be sent to the
`pysam user group <http://groups.google.com/group/pysam-user-group>`_
.. _samtools: http://samtools.sourceforge.net/
.. _tabix: http://samtools.sourceforge.net/tabix.shtml
.. _Li 2009: http://www.ncbi.nlm.nih.gov/pubmed/19505943
.. |build-status| image:: https://travis-ci.org/pysam-developers/pysam.svg
:alt: build status
:scale: 100%
:target: https://travis-ci.org/pysam-developers/pysam
.. |docs| image:: https://readthedocs.org/projects/pysam/badge/?version=latest
:alt: Documentation Status
:scale: 100%
:target: https://pysam.readthedocs.org/en/latest/?badge=latest
|
