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pysam: htslib interface for python
==================================
:Author: Andreas Heger, Kevin Jacobs and contributors
:Date: |today|
:Version: |version|
Pysam is a python module for reading, manipulating and writing
genomic data sets.
Pysam is a wrapper of the htslib_ C-API and provides facilities to
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well
as access to the command line functionality of the samtools_ and
bcftools_ packages. The module supports compression and random access
through indexing.
This module provides a low-level wrapper around the htslib_ C-API as
using cython and a high-level, pythonic API for convenient access to
the data within genomic file formats.
The current version wraps *htslib-1.16*, *samtools-1.16.1*, and *bcftools-1.16*.
To install the latest release, type::
pip install pysam
See the :ref:`Installation notes <installation>` for details.
Contents
--------
.. toctree::
:maxdepth: 2
api.rst
usage.rst
installation.rst
faq.rst
developer.rst
release.rst
benchmarking.rst
glossary.rst
Indices and tables
------------------
Contents:
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
References
----------
.. [Li.2009] *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 `btp352 <https://doi.org/10.1093/bioinformatics/btp352>`_.
PMID: `19505943 <https://pubmed.ncbi.nlm.nih.gov/19505943>`_.
.. [Bonfield.2021] *HTSlib: C library for reading/writing high-throughput sequencing data.*
Bonfield JK, Marshall J, Danecek P, Li H, Ohan V, Whitwham A, Keane T, Davies RM.
GigaScience (2021) 10(2) `giab007 <https://doi.org/10.1093/gigascience/giab007>`_.
PMID: `33594436 <https://pubmed.ncbi.nlm.nih.gov/33594436>`_.
.. [Danecek.2021] *Twelve years of SAMtools and BCFtools.*
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H.
GigaScience (2021) 10(2) `giab008 <https://doi.org/10.1093/gigascience/giab008>`_.
PMID: `33590861 <https://pubmed.ncbi.nlm.nih.gov/33590861>`_.
.. seealso::
Information about htslib
http://www.htslib.org
The samtools homepage
http://samtools.sourceforge.net
The cython C-extensions for python
https://cython.org/
The python language
https://www.python.org
|
