Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids.

ABSTRACT:

Background

Haplotype assembly is the task of reconstructing haplotypes of an individual from a mixture of sequenced chromosome fragments. Haplotype information enables studies of the effects of genetic variations on an organism's phenotype. Most of the mathematical formulations of haplotype assembly are known to be NP-hard and haplotype assembly becomes even more challenging as the sequencing technology advances and the length of the paired-end reads and inserts increases. Assembly of haplotypes polyploid organisms is considerably more difficult than in the case of diploids. Hence, scalable and accurate schemes with provable performance are desired for haplotype assembly of both diploid and polyploid organisms.

Results

We propose a framework that formulates haplotype assembl

SUBMITTER: Hashemi A 

PROVIDER: S-EPMC5872563 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature