HTSeq: High-throughput sequence analysis in Python

Author:Fabio Zanini, Simon Anders and contributors
Date:Oct 28, 2021

HTSeq is a Python package for high-throughput sequencing assays.


HTSeq is described in the following publications:

Fabio Zanini et al.
HTSeq 2.0 – Efficient manipulation of high-throughput sequencing data with long genomes
in preparation (2021)

If you use HTSeq in research, please cite this paper in your publication. I’ve maintained and developed the package for 5 years and it really helps if you cite the paper. Thank you!

The original package is described in:

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


Indices and tables


HTSeq is currently developed by:


HTSeq is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

The full text of the GNU General Public License, version 3, can be found here: