Journal
GENOME BIOLOGY
Volume 16, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-015-0806-y
Keywords
Chromatin conformation; Normalization; Software; Spatial organization; Scalable; Galaxy
Funding
- National Institutes of Health [R01GM035463, R01DK065806]
- American Recovery and Reinvestment Act (ARRA) [RC2HG005542]
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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/.
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