Abstract
BACKGROUND: Chromatin loops are an essential factor in the structural organization of the genome; however, their detection in Hi-C interaction matrices is a challenging and compute-intensive task. The approach presented here, integrated into the HiCExplorer software, shows a chromatin loop detection algorithm that applies a strict candidate selection based on continuous negative binomial distributions and performs a Wilcoxon rank-sum test to detect enriched Hi-C interactions. RESULTS: HiCExplorer's loop detection has a high detection rate and accuracy. It is the fastest available CPU implementation and utilizes all threads offered by modern multicore platforms. CONCLUSIONS: HiCExplorer's method to detect loops by using a continuous negative binomial function combined with the donut approach from HiCCUPS leads to reliable and fast computation of loops. All the loop-calling algorithms investigated provide differing results, which intersect by $\sim 50\%$ at most. The tested in situ Hi-C data contain a large amount of noise; achieving better agreement between loop calling algorithms will require cleaner Hi-C data and therefore future improvements to the experimental methods that generate the data.