Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data

• DOI: 10.1093/bioinformatics/btu747
• Publication Date: 2014-11-13T05:02:10Z
• Authors: Wenyuan Li; Ke Gong; Qingjiao Li; Frank Alber; Xianghong Jasmine...
• Keywords: Normalization; Auxiliary memory; Speedup; Memory hierarchy

Abstract Summary: Genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC, have recently become important tools to study spatial genome organization. Removing biases from chromatin contact matrices generated by such techniques is a critical preprocessing step of subsequent analyses. The continuing decline sequencing costs has led an ever-improving resolution the data, resulting in very large contacts. Such large-size matrices, however, pose great challenge on memory usage speed normalization. Therefore, there urgent need for fast memory-efficient methods normalization data. We developed Hi-Corrector, easy-to-use, open source implementation data algorithm. Its salient features are (i) scalability—the software capable normalizing any size reasonable times; (ii) efficiency—the sequential version can run single computer with limited memory, no matter how little; (iii) speed—the parallel multiple computing nodes local memory. Availability implementation: implemented ANSI C be easily compiled system; MPI library (a standardized portable environment designed solving large-scale scientific problems). package freely available at http://zhoulab.usc.edu/Hi-Corrector/. Contact: [e-mail] or [e-mail] Supplementary information: Bioinformatics online.