Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads

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...

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Bibliographic Details
Published in:arXiv.org 2015-02
Main Authors: Kamath, Govinda M, Eren \c{S}aşoğlu, Tse, David
Format: Article
Language:English
Subjects:
Assembly
Chromosomes
Decoding
Haplotypes
Homology
Polymorphism
Online Access:Get full text
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Summary: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.
ISSN:2331-8422