VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.
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DOI：
10.1093/bioinformatics/btu828
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发表时间：
2015-05-01
期刊：
影响因子：
--
通讯作者：
Lam HY
中科院分区：
文献类型：
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作者：
Mu JC;Mohiyuddin M;Li J;Bani Asadi N;Gerstein MB;Abyzov A;Wong WH;Lam HY
摘要：VarSim是一个框架，用于通过模拟或真实数据评估高通量基因组测序中的比对和变量调用准确性。与模拟随机突变谱不同，它基于现实模型合成具有种系和体细胞突变的二倍体基因组。这个模型利用之前报道的突变等信息，使合成的基因组具有生物学相关性。VarSim模拟和验证了广泛的变种，包括单核苷酸变种、小Indels和大结构变种。它是一个自动化、全面的计算框架，支持并行计算和多个读取模拟器。此外，我们开发了一种新的地图数据结构来验证读取比对，一种策略来比较大小范围内的变量，以及一个轻量级、交互式的图形报告来可视化验证结果和详细的统计数据。到目前为止，它是下一代测序中二次分析最全面的验证工具。可获得性和实现：http://bioinform.github.io/varsim.上提供了用JAVA和PYTHON编写的代码以及下载Reads和变体的说明联系方式：rd@bina.com补充信息：补充数据可从BioInformation Online获得。
Summary: VarSim is a framework for assessing alignment and variant calling accuracy in high-throughput genome sequencing through simulation or real data. In contrast to simulating a random mutation spectrum, it synthesizes diploid genomes with germline and somatic mutations based on a realistic model. This model leverages information such as previously reported mutations to make the synthetic genomes biologically relevant. VarSim simulates and validates a wide range of variants, including single nucleotide variants, small indels and large structural variants. It is an automated, comprehensive compute framework supporting parallel computation and multiple read simulators. Furthermore, we developed a novel map data structure to validate read alignments, a strategy to compare variants binned in size ranges and a lightweight, interactive, graphical report to visualize validation results with detailed statistics. Thus far, it is the most comprehensive validation tool for secondary analysis in next generation sequencing. Availability and implementation: Code in Java and Python along with instructions to download the reads and variants is at http://bioinform.github.io/varsim. Contact: rd@bina.com Supplementary information: Supplementary data are available at Bioinformatics online.
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