HTSeq: High-throughput sequence analysis in Python


Fabio Zanini, Simon Anders, Givanna Putri and contributors


Dec 14, 2023



HTSeq is a Python package for analysis of high-throughput sequencing data.


If you use HTSeq in your research, please cite this paper:

G Putri, S Anders, PT Pyl, JE Pimanda, F Zanini
Analysing high-throughput sequencing data in Python with HTSeq 2.0


bioRxiv previously rejected this preprint saying it’s not proper research. Thankfully, the arXiv was a little more supportive of open source and open science.

HTSeq 1.0 was 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: