HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
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DOI：
10.1186/s13059-015-0831-x
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发表时间：
2015-12-01
期刊：
影响因子：
12.3
通讯作者：
Barillot E
中科院分区：
文献类型：
--
作者：
Servant N;Varoquaux N;Lajoie BR;Viara E;Chen CJ;Vert JP;Heard E;Dekker J;Barillot E
HiC-Pro是一个优化和灵活的管道，用于处理从原始读数到标准化接触图的Hi-C数据。HiC-Pro图谱读取、检测有效连接产物、执行质量控制并生成染色体内和染色体间接触图谱。它包括迭代校正方法的快速实现，并基于Hi-C接触图的内存高效数据格式。此外，HiC-Pro可以使用分阶段基因型数据来构建等位基因特异性接触图谱。我们将HiC-Pro应用于不同的Hi-C数据集，证明了它能够在合理的时间内轻松处理大数据。源代码和文档可在http://github.com/nservant/HiC-Pro上获得。本文的在线版本（doi：10.1186/s13059-015-0831-x）包含补充材料，可供授权用户使用。
HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro. The online version of this article (doi:10.1186/s13059-015-0831-x) contains supplementary material, which is available to authorized users.