HiFive: a tool suite for easy and efficient HiC and 5C data analysis.
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/ .
Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.
Michael Eg
ME
Sauria
Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19103, USA.
Jennifer E
JE
Phillips-Cremins
Department of Biology, Emory University, Atlanta, GA, 30322, USA.
Victor G
VG
Corces
Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA. james@taylorlab.org.
James
J
Taylor
D000465:Algorithms; D002843:Chromatin / Q000737:chemistry*; D023281:Genomics / Q000379:methods; D012984:Software
D002843:Chromatin