Minimum error correction-based haplotype assembly: Considerations for long read data.

Détails

ID Serval
serval:BIB_38E50ECCDCEA
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Minimum error correction-based haplotype assembly: Considerations for long read data.
Périodique
PloS one
Auteur⸱e⸱s
Majidian S., Kahaei M.H., de Ridder D.
ISSN
1932-6203 (Electronic)
ISSN-L
1932-6203
Statut éditorial
Publié
Date de publication
2020
Peer-reviewed
Oui
Volume
15
Numéro
6
Pages
e0234470
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Résumé
The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the genome-phenotype association. Haplotype assembly is a well-known approach for reconstructing haplotypes, exploiting reads generated by DNA sequencing devices. The Minimum Error Correction (MEC) metric is often used for reconstruction of haplotypes from reads. However, problems with the MEC metric have been reported. Here, we investigate the MEC approach to demonstrate that it may result in incorrectly reconstructed haplotypes for devices that produce error-prone long reads. Specifically, we evaluate this approach for devices developed by Illumina, Pacific BioSciences and Oxford Nanopore Technologies. We show that imprecise haplotypes may be reconstructed with a lower MEC than that of the exact haplotype. The performance of MEC is explored for different coverage levels and error rates of data. Our simulation results reveal that in order to avoid incorrect MEC-based haplotypes, a coverage of 25 is needed for reads generated by Pacific BioSciences RS systems.
Mots-clé
Data Analysis, Electronic Data Processing/methods, Genome, Human, Haplotypes/genetics, Humans, Polymorphism, Single Nucleotide/genetics, Scientific Experimental Error, Sequence Analysis, DNA/instrumentation, Sequence Analysis, DNA/methods
Pubmed
Web of science
Open Access
Oui
Création de la notice
16/06/2021 13:26
Dernière modification de la notice
19/10/2023 9:47
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