HTSeq: High-throughput sequence analysis in Python

Author:Fabio Zanini, Simon Anders, Givanna Putri and contributors Date:May 15, 2023 Version:2.0.3

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

• For a high-level description of the package, see the Overview.
• For downloads and installation instructions, see Installation.
• For a thorough example, see A tour through HTSeq.
• For tutorials about specific analyses, see Tutorials.
• For documentation on htseq-count, see htseq-count: counting reads within features.
• Reference API documentation is available on the other pages.

Citation

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

https://doi.org/10.1093/bioinformatics/btac166 (2022)

Note

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

• Index
• Module Index
• Search Page

Authors

HTSeq is currently developed by:

• Givanna Putri at UNSW Sydney (g dot putri at unsw dot edu dot au)
• Simon Anders (anders at embl dot de) at EMBL Heidelberg (Genome Biology Unit).
• Fabio Zanini at UNSW Sydney (fabio dot zanini at unsw dot edu dot au)

License

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: http://www.gnu.org/licenses/gpl-3.0-standalone.html

Sitemap

• Home
• Overview
• Installation
• A tour through HTSeq
• Tutorials
• Counting reads
• Reference API
• Sequences and FASTA/FASTQ files
• Positions, intervals and arrays
• Read alignments
• Features
• Other parsers
• Miscellaneous
• htseq-count: counting reads within features
• htseq-count-barcodes: counting reads with cell barcodes and UMIs
• Quality Assessment with htseq-qa
• Version history
• Contributing