HTSeq – A Python framework to work with high-throughput sequencing data

• DOI: 10.1101/002824
• Publication Date: 2014-02-21T04:59:31Z
• Authors: Simon Anders; Paul Theodor Pyl; Wolfgang Huber
• Keywords: Python

ABSTRACT Motivation: A large choice of tools exists for many standard tasks in the analysis high-throughput sequencing (HTS) data. However, once a project deviates from work flows, custom scripts are needed. Results: We present HTSeq, Python library to facilitate rapid development such scripts. HTSeq offers parsers common data formats HTS projects, as well classes represent genomic coordinates, sequences, reads, alignments, gene model information, variant calls, and provides structures that allow querying via coordinates. also htseq-count, tool developed with preprocesses RNA-Seq differential expression by counting overlap reads genes. Availability: is released open-source software under GNU General Public Licence available http://www-huber.embl.de/HTSeq or Package Index https://pypi.python.org/pypi/HTSeq . Contact: [e-mail]