A graph-based approach to diploid genome assembly.
Bioinformatics
; 34(13): i105-i114, 2018 07 01.
Article
em En
| MEDLINE
| ID: mdl-29949989
ABSTRACT
Motivation Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in health and disease. Current assembly approaches often collapse the two sequences into one haploid consensus sequence and, therefore, fail to capture the diploid nature of the organism under study. Thus, building an assembler capable of producing accurate and complete diploid assemblies, while being resource-efficient with respect to sequencing costs, is a key challenge to be addressed by the bioinformatics community. Results:
We present a novel graph-based approach to diploid assembly, which combines accurate Illumina data and long-read Pacific Biosciences (PacBio) data. We demonstrate the effectiveness of our method on a pseudo-diploid yeast genome and show that we require as little as 50× coverage Illumina data and 10× PacBio data to generate accurate and complete assemblies. Additionally, we show that our approach has the ability to detect and phase structural variants. Availability and implementation https//github.com/whatshap/whatshap. Supplementary information Supplementary data are available at Bioinformatics online.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Genoma Fúngico
/
Análise de Sequência de DNA
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Diploide
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2018
Tipo de documento:
Article
País de afiliação:
Alemanha