PT  - JOURNAL ARTICLE
AU  - Govinda M. Kamath
AU  - Eren Şaşoğlu
AU  - David Tse
TI  - Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads
AID  - 10.1101/014993
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 014993
4099  - http://biorxiv.org/content/early/2015/02/07/014993.short
4100  - http://biorxiv.org/content/early/2015/02/07/014993.full
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.