Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model
Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model
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DOI：
10.1186/1471-2105-13-303
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发表时间：
2012-11-15
影响因子：
3
通讯作者：
Clement, Lieven
中科院分区：
文献类型：
--
作者：
De Beuf, Kristof;De Schrijver, Joachim;Clement, Lieven
背景资料：454焦磷酸测序是一种常用的大规模并行DNA测序技术，具有广泛的应用领域，如表观遗传学，宏基因组学和转录组学。该平台的一个众所周知的问题是其对碱基调用插入和缺失错误的敏感性，特别是在长均聚物存在的情况下。此外，碱基判定质量分数对于插入或缺失错误是否更可能没有信息。令人惊讶的是，没有太多的努力一直致力于改进的碱基调用方法和更直观的质量scores for this platform.Results的发展：我们提出HPCall，一个454碱基调用方法的基础上加权跨栏泊松模型。HPCall使用概率框架通过对众所周知的454个噪声预测因子进行建模来调用序列中的均聚物长度。碱基调用质量评估的基础上估计的概率为每个均聚物的长度，这是很容易转化为有用的质量scores.Conclusions：使用参考数据集的大肠杆菌K-12菌株，我们表明，HPCall产生上级质量分数，是非常翔实的可能的插入和删除错误，同时保持一个碱基调用的准确性，是比目前更好。考虑到框架的通用性，HPCall也有可能适应其他均聚物敏感的测序技术。
Background: 454 pyrosequencing is a commonly used massively parallel DNA sequencing technology with a wide variety of application fields such as epigenetics, metagenomics and transcriptomics. A well-known problem of this platform is its sensitivity to base-calling insertion and deletion errors, particularly in the presence of long homopolymers. In addition, the base-call quality scores are not informative with respect to whether an insertion or a deletion error is more likely. Surprisingly, not much effort has been devoted to the development of improved base-calling methods and more intuitive quality scores for this platform.Results: We present HPCall, a 454 base-calling method based on a weighted Hurdle Poisson model. HPCall uses a probabilistic framework to call the homopolymer lengths in the sequence by modeling well-known 454 noise predictors. Base-calling quality is assessed based on estimated probabilities for each homopolymer length, which are easily transformed to useful quality scores.Conclusions: Using a reference data set of the Escherichia coli K-12 strain, we show that HPCall produces superior quality scores that are very informative towards possible insertion and deletion errors, while maintaining a base-calling accuracy that is better than the current one. Given the generality of the framework, HPCall has the potential to also adapt to other homopolymer-sensitive sequencing technologies.