FastHiC: A Fast Algorithm to Detect Long-Range Chromosomal Interactions from Hi-C Data

FastHiC is a novel hidden Markov random field (HMRF)-based peak caller to detect long-range chromosomal interactions from Hi-C data. In real Hi-C data analysis, FastHiC runs around ten times faster than our previous Bayesian version peak caller HMRFBayes (Xu et al., Bioinformatics, 2015). The substantial speed-up comes from a novel implementation of simulated field approximation, which approximates the joint distribution of the hidden peak status by a set of independent random variables, leading to more tractable computation. The current version is a pre-release. For details, please refer to our tutorial.

Comments and suggestions are welcome, please e-mail Zheng Xu at xuzheng@email.unc.edu or Ming Hu at hum@ccf.org or Yun Li at yunli@med.unc.edu.