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This package is no longer being actively maintained; feel free to post issues that others in the community may respond to, but this package will likely not be updated further. Additionally, if anyone wants to maintain a fork of the package or has developed an alternative package for similar purposes, would be happy to link to that repo here.

Python package for calling nucleosomes using ATAC-seq data. Also includes general scripts for working with paired-end ATAC-seq data (or potentially other paired-end data).

Please cite our paper at Genome Research if you use this tool in your research.

Please use GitHub Issues to bring up any errors that occur with software rather than emailing authors.

Note on Versions:

  • version 0 represents code used for biorxiv manuscript
  • version 0.2.1 was used for Genome Research manuscript (See Supplemental Information as well)

Documentation can be found at

If you want to easily read in NucleoATAC outputs into R for further processing or exploration, check out NucleoATACR

Currently NucleoATAC only supports Python 2.7 (No Python 3). If anyone is interested in adding Python 3 support, pull requests welcome 😄