RT Journal Article
SR Electronic
T1 Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 014993
DO 10.1101/014993
A1 Govinda M. Kamath
A1 Eren Şaşoğlu
A1 David Tse
YR 2015
UL http://biorxiv.org/content/early/2015/02/07/014993.abstract
AB 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.