HiFive: a tool suite for easy and efficient HiC and 5C data analysis

• Type of Material: Article
• Authors: Michael EG Sauria, Johns Hopkins University; Jennifer E. Phillips-Cremins, University of Pennsylvania; Victor Corces, Emory University; James Taylor, Johns Hopkins University
• Language: English
• Date: 2015-10-24
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: © Sauria et al. 2015
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1186/s13059-015-0806-y
• Title of Journal or Parent Work: Genome Biology
• Volume: 16
• Issue: 237
• Grant/Funding Information: National Institute of General Medical Sciences R01GM035463 to Victor G. Corces.; National Human Genome Research Institute RC2HG005542 to James Taylor.; National Institute of Diabetes and Digestive and Kidney Diseases R01DK065806 to James Taylor.
• Keywords: Normalization; Software; Scalable; Chromatin conformation; Galaxy; Spatial organization
• Research Categories: Biology, General

Abstract

The chromatin interaction assays 5C and HiC have advanced our understanding of genomic spatial organization, but analysis approaches for these data are limited by usability and flexibility. The HiFive tool suite provides efficient data handling and a variety of normalization approaches for easy, fast analysis and method comparison. Integration of MPI-based parallelization allows scalability and rapid processing time. In addition to single-command analysis of an entire experiment from mapped reads to interaction values, HiFive has been integrated into the open-source, web-based platform Galaxy to connect users with computational resources and a graphical interface. HiFive is open-source software available from http://taylorlab.org/software/hifive/.