HiCExplorer - a suite of tools for reproducible Hi-C data analysis, quality control and visualization


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Hi-C has become a standard technique for the genome-wide analysis of chromosome conformation. Analysis of Hi-C data provides insights into folding principles of the chromatin, functional compartments within the nucleus, as well as long range enhancer-promoter interactions. Integration of Hi-C and other epigenomic datasets has helped researchers in understanding of mechanisms of gene regulation and genetic diseases.

Today we released HiCExplorer 2.0 to provide an easy and user-friendly access to the analysis of Hi-C data. Starting with the mapping of the raw sequence data, creation of the contact matrices, the correction of contact matrices, to the computation of topological associated domains (TADs) and A/B compartments. A detailed quality report generated during the process, which, using the support of MultiQC, allows users to compare multiple Hi-C datasets. Finally, the users can create publication ready plots of the contact matrix, A/B compartments, and TADs on a selected genomic locus, along with additional information like gene tracks or ChIP-Seq signals.

A template workflow is shared with everyone and an example history is also available.

For more detailed information check out the HiCExplorer GitHub repository, our Galaxy Docker flavor or two publication were it was used already:

Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening, Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke, High-resolution TADs reveal DNA sequences underlying genome organization in flies

Ralf Gilsbach, Martin Schwaderer, Sebastian Preissl, Bjoern A Gruening, David Kranzhoefer, et al., Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo.

Of course all tools are available from the Galaxy ToolShed and installable into any Galaxy instance.