SpecHap: a diploid phasing algorithm based on spectral graph theory.
Nucleic Acids Res
; 49(19): e114, 2021 11 08.
Article
em En
| MEDLINE
| ID: mdl-34403470
ABSTRACT
Haplotype phasing plays an important role in understanding the genetic data of diploid eukaryotic organisms. Different sequencing technologies (such as next-generation sequencing or third-generation sequencing) produce various genetic data that require haplotype assembly. Although multiple diploid haplotype phasing algorithms exist, only a few will work equally well across all sequencing technologies. In this work, we propose SpecHap, a novel haplotype assembly tool that leverages spectral graph theory. On both in silico and whole-genome sequencing datasets, SpecHap consumed less memory and required less CPU time, yet achieved comparable accuracy with state-of-art methods across all the test instances, which comprises sequencing data from next-generation sequencing, linked-reads, high-throughput chromosome conformation capture, PacBio single-molecule real-time, and Oxford Nanopore long-reads. Furthermore, SpecHap successfully phased an individual Ambystoma mexicanum, a species with gigantic diploid genomes, within 6 CPU hours and 945MB peak memory usage, while other tools failed to yield results either due to memory overflow (40GB) or time limit exceeded (5 days). Our results demonstrated that SpecHap is scalable, efficient, and accurate for diploid phasing across many sequencing platforms.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Genoma
/
Análise de Sequência de DNA
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Sequenciamento de Nucleotídeos em Larga Escala
/
Ambystoma mexicanum
/
Sequenciamento Completo do Genoma
Tipo de estudo:
Prognostic_studies
Limite:
Animals
/
Humans
Idioma:
En
Revista:
Nucleic Acids Res
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
China