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htseq website  

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

See the HTSeq documentation chapter A tour through HTSeq first for an overview on the kind of analysis you can do with HTSeq and the design of the package, and then look at the reference documentation.

While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge. See the Scripts section in the overview below for what is available.

Required Modules

modules documentation


  • htseq

System Variables

  • HPC_HTSEQ_DIR - installation directory
  • HPC_HTSEQ_BIN - executable directory.

Additional Information

Two programs are available - htseq-count and htseq-qa. Run them without any arguments to see the usage information. The main HTSeq module can be loaded from python (import HTSeq). See HTSeq documentation for a tutorial.


If you publish research that uses {{{app}}} you have to cite it as follows:

Simon Anders, Paul Theodor Pyl, Wolfgang Huber HTSeq — A Python framework to work with high-throughput sequencing data Bioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638.


  • Validated 4/5/2018