Introduction

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 of sequencing costs has led to an ever-improving resolution of the Hi-C data, resulting in very large matrices of chromatin contacts. Such large-size matrices, however, pose a great challenge on the memory usage and speed of its normalization. Therefore, there is an urgent need for fast and memory-efficient methods for normalization of Hi-C data. We developed Hi-Corrector, an easy-to-use, open source implementation of the Hi-C data normalization algorithm. Its salient features are (i) scalability-the software is capable of normalizing Hi-C data of any size in reasonable times; (ii) memory efficiency-the sequential version can run on any single computer with very limited memory, no matter how little; (iii) fast speed-the parallel version can run very fast on multiple computing nodes with limited local memory.The sequential version is implemented in ANSI C and can be easily compiled on any system; the parallel version is implemented in ANSI C with the MPI library (a standardized and portable parallel environment designed for solving large-scale scientific problems). The package is freely available at http://zhoulab.usc.edu/Hi-Corrector/.

Publications

  1. Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.
    Cite this
    Li W, Gong K, Li Q, Alber F, Zhou XJ, 2015-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Wenyuan Li
    Developer

    Molecular and Computational Biology Program, Department of Biological Sciences, United States of America

  2. Ke Gong
    Developer

    Molecular and Computational Biology Program, Department of Biological Sciences, United States of America

  3. Qingjiao Li
    Developer

    Molecular and Computational Biology Program, Department of Biological Sciences, United States of America

  4. Frank Alber
    Developer

    Molecular and Computational Biology Program, Department of Biological Sciences, United States of America

  5. Xianghong Jasmine Zhou
    Investigator

    Molecular and Computational Biology Program, Department of Biological Sciences, United States of America

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Summary
AccessionBT003267
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByXianghong Jasmine Zhou