HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Table 1 Comparing solutions for Hi-C data processing

	Mapping	Detection of valid interactions	Binning	Correction of systematic noise	Parallel implementation	Allele-specific analysis
HOMER		x	x
HICUP	x	x				x
HiC-inspector	x^a	x	x
HiC-Box	x^a	x	x	x
HiCdat	x^a	x	x	x
Hiclib	x	x	x	x
HiC-Pro	x	x	x	x	x	x

HOMER [10] offers several programs to analysis Hi-C data from aligned reads. ^aHiC-inpector [12], HiCdat [13] and HiC-Box [14] do not allow chimeric reads to be rescued during the mapping. HICUP [11] provides a complete pipeline until the detection of valid interaction products. It can be used together with the SNPsplit software [15] to extract allele-specific mapped reads. The hiclib Python library [17] can be applied for all analysis steps but requires good programming skills and cannot be used in a single command-line manner. None of these software enable very large amounts of data to be processed easily in a parallel mode. Note that HOMER, hiclib and HiCdat also offer additional functions for downstream analysis. In the case of HiC-Pro, the downstream analysis is supported by the HiTC BioConductor package [28]

ISSN: 1474-760X