Jiang Rong, Tavaré Simon, Marjoram Paul
Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK.
Genetics. 2009 Jan;181(1):187-97. doi: 10.1534/genetics.107.080630. Epub 2008 Nov 3.
This article is concerned with statistical modeling of shotgun resequencing data and the use of such data for population genetic inference. We model data produced by sequencing-by-synthesis technologies such as the Solexa, 454, and polymerase colony (polony) systems, whose use is becoming increasingly widespread. We show how such data can be used to estimate evolutionary parameters (mutation and recombination rates), despite the fact that the data do not necessarily provide complete or aligned sequence information. We also present two refinements of our methods: one that is more robust to sequencing errors and another that can be used when no reference genome is available.
本文关注鸟枪法重测序数据的统计建模以及此类数据在群体遗传推断中的应用。我们对诸如Solexa、454和聚合酶克隆（polony）系统等合成测序技术产生的数据进行建模，这些技术的应用正日益广泛。我们展示了如何利用此类数据来估计进化参数（突变率和重组率），尽管这些数据不一定能提供完整或比对好的序列信息。我们还提出了对我们方法的两项改进：一项对测序错误更具鲁棒性，另一项可在没有参考基因组时使用。
