NGS based haplotype assembly using matrix completion.
Details
Serval ID
serval:BIB_2CB13C2442BE
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
NGS based haplotype assembly using matrix completion.
Journal
PloS one
ISSN
1932-6203 (Electronic)
ISSN-L
1932-6203
Publication state
Published
Issued date
2019
Peer-reviewed
Oui
Volume
14
Number
3
Pages
e0214455
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Publication Status: epublish
Abstract
We apply matrix completion methods for haplotype assembly from NGS reads to develop the new HapSVT, HapNuc, and HapOPT algorithms. This is performed by applying a mathematical model to convert the reads to an incomplete matrix and estimating unknown components. This process is followed by quantizing and decoding the completed matrix in order to estimate haplotypes. These algorithms are compared to the state-of-the-art algorithms using simulated data as well as the real fosmid data. It is shown that the SNP missing rate and the haplotype block length of the proposed HapOPT are better than those of HapCUT2 with comparable accuracy in terms of reconstruction rate and switch error rate. A program implementing the proposed algorithms in MATLAB is freely available at https://github.com/smajidian/HapMC.
Keywords
Algorithms, Benchmarking, Cosmids/genetics, Haplotypes/genetics, High-Throughput Nucleotide Sequencing, Models, Genetic, Polymorphism, Single Nucleotide
Pubmed
Web of science
Open Access
Yes
Create date
16/06/2021 13:26
Last modification date
19/10/2023 9:47