iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization.
iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization.
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DOI：
10.1371/journal.pone.0195334
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Parekh N
中科院分区：
文献类型：
--
作者：
Dharanipragada P;Vogeti S;Parekh N
拷贝数变异(CNV)是一大类结构变异，它的发现极大地改变了我们对个体差异的理解，为人类疾病的遗传基础提供了另一种范式。CNV既包括拷贝增加事件，也包括拷贝丢失事件，现在可以使用高通量、低成本的下一代测序(NGS)方法在全基因组范围内检测CNV。然而，从NGS数据中准确检测CNV并非易事，因为各种系统性偏差导致的读数覆盖率不一致。我们已经开发了一个集成平台iCopyDAV，用于处理全基因组NGS数据中CNV检测的一些问题。它有一个模块化的框架，包括五个主要模块：数据预处理、分割、变量调用、标注和可视化。ICopyDAV的一个重要功能是功能注释模块，它使用户能够识别包含各种功能元件、基因组特征和疾病关联的CNV并确定其优先顺序。分割算法的并行化使iCopyDAV平台甚至可以在桌面上访问。在这里，我们展示了测序覆盖率、读取长度、条带大小、数据预处理和分割方法对准确检测CNV全谱的影响。在不同测序深度的模拟数据和实际数据上对iCopyDAV的性能进行了评估。这是一个开源的集成管道，可以在https://github.com/vogetihrsh/icopydav上使用，也可以在http://bioinf.iiit.ac.in/icopydav/.上使用Docker的形象
Discovery of copy number variations (CNVs), a major category of structural variations, have dramatically changed our understanding of differences between individuals and provide an alternate paradigm for the genetic basis of human diseases. CNVs include both copy gain and copy loss events and their detection genome-wide is now possible using high-throughput, low-cost next generation sequencing (NGS) methods. However, accurate detection of CNVs from NGS data is not straightforward due to non-uniform coverage of reads resulting from various systemic biases. We have developed an integrated platform, iCopyDAV, to handle some of these issues in CNV detection in whole genome NGS data. It has a modular framework comprising five major modules: data pre-treatment, segmentation, variant calling, annotation and visualization. An important feature of iCopyDAV is the functional annotation module that enables the user to identify and prioritize CNVs encompassing various functional elements, genomic features and disease-associations. Parallelization of the segmentation algorithms makes the iCopyDAV platform even accessible on a desktop. Here we show the effect of sequencing coverage, read length, bin size, data pre-treatment and segmentation approaches on accurate detection of the complete spectrum of CNVs. Performance of iCopyDAV is evaluated on both simulated data and real data for different sequencing depths. It is an open-source integrated pipeline available at https://github.com/vogetihrsh/icopydav and as Docker’s image at http://bioinf.iiit.ac.in/icopydav/.
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DOI：
10.1093/bioinformatics/btr670
发表时间：
2012-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
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作者：
Boeva V;Popova T;Bleakley K;Chiche P;Cappo J;Schleiermacher G;Janoueix-Lerosey I;Delattre O;Barillot E
通讯作者：
Barillot E
影响因子：
7
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通讯作者：
Hubbard TJ
影响因子：
3.7
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Derrien T;Estellé J;Marco Sola S;Knowles DG;Raineri E;Guigó R;Ribeca P
通讯作者：
Ribeca P
影响因子：
50.3
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Hu X;Feng Y;Zhang D;Zhao SD;Hu Z;Greshock J;Zhang Y;Yang L;Zhong X;Wang LP;Jean S;Li C;Huang Q;Katsaros D;Montone KT;Tanyi JL;Lu Y;Boyd J;Nathanson KL;Li H;Mills GB;Zhang L
通讯作者：
Zhang L
影响因子：
64.8
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