HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking

BMC Genomics

Table 2 The HiC-bench toolkit

Hi-C tasks	HiC-bench toolkit
Alignment	bowtie2, gtools-hic[align]
Filtering	gtools-hic[filter]
Genome browser tracks	gtools-hic[bin/convert]
Matrix generation	gtools-hic[matrix]
Matrix correction	IC, HiCNorm, hic-matrix[preprocess/normalize]
Boundary scores	hic-matrix[domains]
Domain calling	DI, Armatus, TopDom, hic-matrix[domains]
Interactions	hic-matrix[loops]
Annotations	genomic-tools
Visualization	HiCPlotter

The HiC-bench toolkit consists mostly of newly-developed tools (shown in bold) but we have also incorporated existing tools to allow comparisons and benchmarking

ISSN: 1471-2164