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Table 2 The HiC-bench toolkit

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

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
  1. 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