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.
- For a high-level description of the package, see the Overview.
- For downloads and installation instructions, see Installation.
- For an example on the kind of analyses you can do with HTSeq and the design of the package, see A tour through HTSeq.
- For documentation on htseq-count, see htseq-count: counting reads within features.
- See the reference documentation for details on specific functions.
HTSeq is described in the following publications:
Fabio Zanini et al.HTSeq 2.0 – Efficient manipulation of high-throughput sequencing data with long genomesin 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 HuberHTSeq — A Python framework to work with high-throughput sequencing dataBioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638
- A tour through HTSeq
- A detailed use case: Transcription start sites
- Counting reads
- Reference overview
- Sequences and FASTA/FASTQ files
- Genomic intervals and genomic 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
- Next version (current master)
- Version 0.13.5
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- Version 0.4.5
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- Version 0.4.3
- Version 0.4.2
- Version 0.4.1
- Version 0.4.0
- Version 0.3.7
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