ParticleCall: a particle filter for base calling in next-generation sequencing systems.
ParticleCall: a particle filter for base calling in next-generation sequencing systems.
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DOI：
10.1186/1471-2105-13-160
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发表时间：
2012-07-09
影响因子：
3
通讯作者：
Vikalo H
中科院分区：
文献类型：
--
作者：
Shen X;Vikalo H
下一代测序系统能够进行快速且具有成本效益的DNA测序，从而实现常规测序任务，并使我们更接近个性化医疗。然而，其读数的准确性和长度尚未超过常规桑格测序方法所提供的那些。这激发了对能够从所获取的数据中可靠且准确地检测短DNA片段中的核苷酸顺序的计算高效算法的搜索。在本文中，我们考虑了Illumina的合成测序平台，该平台依赖于可逆终止剂化学，并通过将其数学模型重新表述为隐马尔可夫模型来描述所获得的信号。依靠这个模型和序贯蒙特卡罗方法，我们开发了一个参数估计和基地调用计划称为ParticleCall。在通过使用Illumina的基因组分析仪II对phiX174噬菌体测序获得的数据集上测试ParticleCall。结果表明，所开发的碱基调用方案比目前可用的最佳无监督方法的计算效率更高，同时达到相同的精度。所提出的ParticleCall提供了比Illumina的碱基调用算法Bustard更准确的调用。与此同时，ParticleCall的计算效率明显高于最近其他具有类似性能的方案，使其更适用于高通量测序数据分析。碱基识别准确性的提高将对下游应用如SNP和基因型识别的性能产生直接的有益影响。ParticleCall可在https://sourceforge.net/projects/particlecall上免费获得。
Next-generation sequencing systems are capable of rapid and cost-effective DNA sequencing, thus enabling routine sequencing tasks and taking us one step closer to personalized medicine. Accuracy and lengths of their reads, however, are yet to surpass those provided by the conventional Sanger sequencing method. This motivates the search for computationally efficient algorithms capable of reliable and accurate detection of the order of nucleotides in short DNA fragments from the acquired data. In this paper, we consider Illumina’s sequencing-by-synthesis platform which relies on reversible terminator chemistry and describe the acquired signal by reformulating its mathematical model as a Hidden Markov Model. Relying on this model and sequential Monte Carlo methods, we develop a parameter estimation and base calling scheme called ParticleCall. ParticleCall is tested on a data set obtained by sequencing phiX174 bacteriophage using Illumina’s Genome Analyzer II. The results show that the developed base calling scheme is significantly more computationally efficient than the best performing unsupervised method currently available, while achieving the same accuracy. The proposed ParticleCall provides more accurate calls than the Illumina’s base calling algorithm, Bustard. At the same time, ParticleCall is significantly more computationally efficient than other recent schemes with similar performance, rendering it more feasible for high-throughput sequencing data analysis. Improvement of base calling accuracy will have immediate beneficial effects on the performance of downstream applications such as SNP and genotype calling. ParticleCall is freely available at https://sourceforge.net/projects/particlecall.
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影响因子：
14.9
作者：
Fedurco, M;Romieu, A;Williams, S;Lawrence, I;Turcatti, G
通讯作者：
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影响因子：
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作者：
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影响因子：
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作者：
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DOI：
10.1049/ip-rsn:19990255
发表时间：
1999-02-01
期刊：
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影响因子：
--
作者：
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通讯作者：
Fearnhead, P
影响因子：
14.9
作者：
Doucet, A;Wang, XD
通讯作者：
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