Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.

Joachim Wolff,Rolf Backofen,Björn A Grüning,Ralf Gilsbach,Gautier Richard,Thomas Manke,Leily Rabbani

doi:10.1093/nar/gkaa220

Abstract

The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data. Since the last publication, Galaxy HiCExplorer has been expanded considerably with new tools to facilitate the analysis of cHi-C and to provide an in-depth analysis of Hi-C data. Moreover, it supports the analysis of scHi-C data by offering a broad range of tools. With the help of the standard graphical user interface of Galaxy, presented workflows, extensive documentation and tutorials, novices as well as Hi-C experts are supported in their Hi-C data analysis with Galaxy HiCExplorer.

Highlights

Chromosome conformation capture (3C) [1] and its successors 4C [2,3], 5C [4] and Hi-C [5] have developed into the standard technologies used in studying the 3D conformation of chromatin
The presented web server on https://hicexplorer.usegalaxy. eu gives researchers the opportunity to focus on their data analysis in a user friendly, reproducible and computationally powerful environment
Galaxy HiCExplorer is suited for both experts and newcomers to the Hi-C field, thanks to the provided tutorials that give all users a clear introduction on how to use HiCExplorer for their data analyses

Summary

INTRODUCTION

Chromosome conformation capture (3C) [1] and its successors 4C [2,3], 5C [4] and Hi-C [5] have developed into the standard technologies used in studying the 3D conformation of chromatin. Hi-C is unable to capture protein-DNA interactions in the chromatin conformation context To overcome these shortcomings, capture Hi-C (cHi-C) techniques have been developed. Galaxy HiCExplorer meets these requirements by providing efficient and easy to use tools for the analysis of Hi-C, cHi-C and scHi-C through a comprehensive and unified web server accessible at https://hicexplorer.usegalaxy.eu. It provides computational capabilities for even the most demanding analyses. A command line version is provided by conda and is available via the bioconda channel [16]

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DISCUSSION