Near-optimal assembly for shotgun sequencing with noisy reads
Near-optimal assembly for shotgun sequencing with noisy reads
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DOI：
10.1186/1471-2105-15-s9-s4
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发表时间：
2014-09-10
影响因子：
3
通讯作者：
Tse, David
中科院分区：
文献类型：
--
作者：
Lam, Ka-Kit;Khalak, Asif;Tse, David
最近的工作基于读取中没有错误（无噪声读取）的理想假设，确定了从鸟枪测序数据成功从头基因组重建所需的读取长度和覆盖深度方面信息要求的基本限制。在这项工作中，我们表明，即使读数中存在噪声，人们也可以成功地重建信息，其信息要求接近无噪声基本极限。一种新的组装算法“X-phased Multibridging”是基于基因组概率模型设计的。通过分析表明它在模型上表现良好，通过模拟在真实基因组上表现良好。
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption of no errors in the reads (noiseless reads). In this work, we show that even when there is noise in the reads, one can successfully reconstruct with information requirements close to the noiseless fundamental limit. A new assembly algorithm, X-phased Multibridging, is designed based on a probabilistic model of the genome. It is shown through analysis to perform well on the model, and through simulations to perform well on real genomes.