Probabilistic base calling of Solexa sequencing data
Probabilistic base calling of Solexa sequencing data
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DOI：
10.1186/1471-2105-9-431
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发表时间：
2008-10-13
影响因子：
3
通讯作者：
Naef, Felix
中科院分区：
文献类型：
--
作者：
Rougemont, Jacques;Amzallag, Arnaud;Naef, Felix
背景资料：Solexa/Illumina短读超高通量DNA测序技术通过DNA菌落的平行合成测序产生数百万个短标签（多达36个碱基）。这样的高通量数据的处理和统计分析提出了新的挑战，目前一个公平的比例的标签被例行丢弃，由于无法将它们匹配到一个参考sequence. Results的，从而降低了有效的吞吐量的technology.Results：我们提出了一种新的基地调用算法，使用基于模型的聚类和概率理论，以确定模糊的基地和代码与IUPAC符号。我们还选择最佳的子标签使用的分数的基础上的信息内容，以消除不确定的碱基对reads.Conclusion的结束：我们表明，该方法提高了基因组的覆盖率和可用的标签数相比，Solexa的数据处理管道平均15%。提供了一个R软件包，可以快速准确地调用Solexa的荧光强度文件，并生成信息丰富的诊断图。
Background: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags ( up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology.Results: We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads.Conclusion: We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.