Feb 7, 2015

Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads

BioRxiv : the Preprint Server for Biology
Govinda M KamathDavid Tse

Abstract

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.

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Mentioned in this Paper

Genome
Mathematical Formula
High Throughput Analysis
Chromosomes
Documented
Analysis
Genetic Polymorphism
Single Nucleotide Polymorphism
Homologous Gene
Molecular Assembly/Self Assembly

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