Skip to main content

A framework to process and analyze data from high-throughput sequencing (HTS) assays

Project description

CI Documentation Status




CITATION (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, (2022).

A Python library to facilitate programmatic analysis of data from high-throughput sequencing (HTS) experiments. A popular component of HTSeq is htseq-count, a script to quantify gene expression in bulk and single-cell RNA-Seq and similar experiments.


To use HTSeq you need:

  • Python >= 3.7 (note: Python 2.7 support has been dropped)
  • numpy
  • pysam

To manipulate BigWig files, you also need:

  • pyBigWig

To run the htseq-qa script, you also need:

  • matplotlib

To run htseq-count and htseq-count-barcodes with custom output formats for the counts table, you need:

  • mtx file: scipy
  • h5ad file: anndata
  • loom file: loompy

Both Linux and OSX are supported and binaries are provided on Pypi. We would like to support Windows but currently lack the expertise to do so. If you would like to take on the Windows release and maintenance, please open an issue and we'll try to help.

A source package which should not require Cython nor SWIG is also provided on Pypi.

To develop HTSeq you will also need:

  • Cython >=0.29.5
  • SWIG >=3.0.8



To install directly from PyPI:

pip install HTSeq

To install a specific version:

pip install 'HTSeq==2.0.0'

If this fails, please install all dependencies first:

pip install matplotlib
pip install Cython
pip install pysam
pip install HTSeq (distutils/setuptools)

Install the dependencies with your favourite tool (pip, conda, etc.).

To install HTSeq itself, run:

python build install


To test locally, run


To test htseq-count alone, run it with the -o option.

A virtual environment is created in the .venv folder and HTSeq is installed inside it, including all modules and scripts.


Project details

Release history Release notifications | RSS feed

This version


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

htseq-2.0.7.tar.gz (466.2 kB view hashes)

Uploaded Source

Built Distributions

HTSeq-2.0.7-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.2 MB view hashes)

Uploaded CPython 3.12 manylinux: glibc 2.17+ x86-64

HTSeq-2.0.7-cp312-cp312-macosx_10_9_x86_64.whl (352.1 kB view hashes)

Uploaded CPython 3.12 macOS 10.9+ x86-64

HTSeq-2.0.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.2 MB view hashes)

Uploaded CPython 3.11 manylinux: glibc 2.17+ x86-64

HTSeq-2.0.7-cp311-cp311-macosx_10_9_x86_64.whl (349.6 kB view hashes)

Uploaded CPython 3.11 macOS 10.9+ x86-64

HTSeq-2.0.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.0 MB view hashes)

Uploaded CPython 3.10 manylinux: glibc 2.17+ x86-64

HTSeq-2.0.7-cp310-cp310-macosx_10_9_x86_64.whl (348.1 kB view hashes)

Uploaded CPython 3.10 macOS 10.9+ x86-64

HTSeq-2.0.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.0 MB view hashes)

Uploaded CPython 3.9 manylinux: glibc 2.17+ x86-64

HTSeq-2.0.7-cp39-cp39-macosx_10_9_x86_64.whl (348.5 kB view hashes)

Uploaded CPython 3.9 macOS 10.9+ x86-64

HTSeq-2.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB view hashes)

Uploaded CPython 3.8 manylinux: glibc 2.17+ x86-64

HTSeq-2.0.7-cp38-cp38-macosx_10_9_x86_64.whl (362.6 kB view hashes)

Uploaded CPython 3.8 macOS 10.9+ x86-64

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page