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, fas...

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Detalles Bibliográficos
Autores principales: Sauria, Michael EG, Phillips-Cremins, Jennifer E., Corces, Victor G., Taylor, James
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5410870/
https://www.ncbi.nlm.nih.gov/pubmed/26498826
http://dx.doi.org/10.1186/s13059-015-0806-y
Descripción
Sumario: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/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0806-y) contains supplementary material, which is available to authorized users.

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