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

Table 3 Performance of iterative correction on IMR90 data

	HiC-Pro – Iced (dense – 1 CPU)	HiC-Pro – Iced (sparse – 1 CPU)	HiCorrector – MES (dense – 1 CPU)	HiCorrector – MEP (dense – 8 CPUs)
IMR90 1Mbp	00:00:12	00:00:25	00:00:25	00:00:06
IMR90 500 kbp	00:00:40	00:01:30	00:02:15	00:00:22
IMR90 150 kbp	-	00:04:28	00:13:21	00:03:10
IMR90 40 kbp	-	00:07:19	02:35:34	00:35:43
IMR90 2 0kbp	-	00:08:36	12:57:17	02:34:05

HiC-Pro is based on a fast implementation of the iterative correction algorithm. We therefore compare our method with the MES (Memory-Efficient Sequential) and MEP (Memory-Efficient Parallel) algorithms of the HiCorrector software [20] for Hi-C data normalization (hours:minutes:seconds). All algorithms were terminated after 20 iterations (see Additional file 1 for details)

ISSN: 1474-760X