RT Journal Article SR Electronic T1 HTSeq – A Python framework to work with high-throughput sequencing data JF bioRxiv FD Cold Spring Harbor Laboratory SP 002824 DO 10.1101/002824 A1 Simon Anders A1 Paul Theodor Pyl A1 Wolfgang Huber YR 2014 UL http://biorxiv.org/content/early/2014/08/19/002824.abstract AB Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard work flows, custom scripts are needed.Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data such as genomic coordinates, sequences, sequencing reads, alignments, gene model information, variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.Availability: HTSeq is released as open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index https://pypi.python.org/pypi/HTSeq.Contact: sanders{at}fs.tum.de