Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads
Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads
复制标题
高通量配对读取的最佳单倍型组装
DOI：
10.1101/014993
复制
发表时间：
2015
期刊：
影响因子：
--
通讯作者：
David Tse
中科院分区：
文献类型：
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作者：
G. Kamath;Eren Sasoglu;David Tse
人类有23对同源染色体。同源对是几乎相同的染色体对。在大多数情况下，同源染色体的差异发生在某些被称为单核苷酸多态性（SNP）的记录位置。个体的单倍型是两个同源染色体上的SNP序列对。在本文中，我们研究的问题，推断单倍型的个人从他们的基因组的配偶对读取。我们给出了一个简单的公式为单倍型组装所需的覆盖率，下生成模型。这里的分析利用了这个问题与解码卷积码的联系。
Humans have 23 pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide polymorphisms (SNPs). A haplotype of an individual is the pair of sequences of SNPs on the two homologous chromosomes. In this paper, we study the problem of inferring haplotypes of individuals from mate-pair reads of their genome. We give a simple formula for the coverage needed for haplotype assembly, under a generative model. The analysis here leverages connections of this problem with decoding convolutional codes.