title: HTSeq--a Python framework to work with high-throughput sequencing data.
abstract: BACKGROUND
  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 workflows, 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 and 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.
  
  
  METHODS
  HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq.
authors.affiliation: Genome Biology Unit, European Molecular Biology Laboratory, 69111 Heidelberg, Germany.
authors.forename: Simon
authors.initials: S
authors.lastname: Anders
authors.affiliation: Genome Biology Unit, European Molecular Biology Laboratory, 69111 Heidelberg, Germany.
authors.forename: Paul Theodor
authors.initials: PT
authors.lastname: Pyl
authors.affiliation: Genome Biology Unit, European Molecular Biology Laboratory, 69111 Heidelberg, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Huber
mesh_terms: D005786:Gene Expression Regulation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012984:Software