基因组重测序深度的计算

ESTIMATING SEQUENCING DEPTH OF NEXT-GENERATION RESEQUENING GENOME DATA

随着第二代测序的发展,基因组重测序已经成为研究动植物分子育种最为快速有效的方法之一。基因组重测序需要高质量地测定每个碱基,同时需要平衡好测序深度与费用的关系。因此,为做好测序深度的估计,本文结合案例给出两种估算模型即基于片段的二项分布模型和基于碱基的泊松分布模型对重测序深度的计算方法进行了分析和推导,从而有利于在教学过程中对这一问题的确切讲解。为收到较好的教学效果,本研究设计了相关模型模拟器并对该课程的理论性与实践性的问题进行了讨论。

With the development of the next - generation sequencing, resequencing has become one of the effective method to study the molecular breeding on animals and plants. Next - generation shotgun resequencing approaches require sequencing every base in a sample several times. It is imperative to address the trade - off between the sequencing depth and cost. Depth of sequencing should be estimated before starting a sequencing experiment. By establishing two statistical models （binomial distribution for fragments and possion distribution for bases） of shotgun sequencing, we can give a good estimation of the necessary depth in genome resequencing. This will provide teachers and learners information on understanding the equation more accurately and choosing appropriate sequencing depth. To get a better teaching effect, main aspect of teaching resequencing applied in population genetics was discussed.