HTSeq: High-throughput sequence analysis in Python
Fabio Zanini, Simon Anders, Givanna Putri and contributors
Nov 22, 2023
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.
If you use HTSeq in your research, please cite this paper:
G Putri, S Anders, PT Pyl, JE Pimanda, F ZaniniAnalysing 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 HuberHTSeq — A Python framework to work with high-throughput sequencing dataBioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638
Indices and tables
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
- A tour through HTSeq
- Counting reads
- Reference API
- Sequences and FASTA/FASTQ files
- Positions, intervals and arrays
- Read alignments
- Other parsers
htseq-count: counting reads within features
htseq-count-barcodes: counting reads with cell barcodes and UMIs
- Quality Assessment with
- Version history