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FAN-C: Framework for the ANalysis of C-like data

FAN-C provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads.

Please check out the documentation at for detailed installation and usage instructions!

FAN-C is published in Genome Biology. If you use it in your research, please cite it as:

Kruse, K., Hug, C.B. & Vaquerizas, J.M. 
FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. 
Genome Biol 21, 303 (2020).

If you like FAN-C, come and say "Hi" on Twitter! @kaukrise @vaquerizas_lab


We are currently working on a much faster version of FAN-C with speedups of more than 10x for many commands. If you want to try it out and give us some feedback, please check out the dev channel. You can find instructions in the docs. Note that this is not an official release yet, however, and you will likely encounter unresolved issues, which we kindly ask you to report here, on GitHub! Thanks!