deBGA: read alignment with de Bruijn graph-based seed and extension.
Bioinformatics
; 32(21): 3224-3232, 2016 11 01.
Article
en En
| MEDLINE
| ID: mdl-27378303
ABSTRACT
MOTIVATION As high-throughput sequencing (HTS) technology becomes ubiquitous and the volume of data continues to rise, HTS read alignment is becoming increasingly rate-limiting, which keeps pressing the development of novel read alignment approaches. Moreover, promising novel applications of HTS technology require aligning reads to multiple genomes instead of a single reference; however, it is still not viable for the state-of-the-art aligners to align large numbers of reads to multiple genomes. RESULTS:
We propose de Bruijn Graph-based Aligner (deBGA), an innovative graph-based seed-and-extension algorithm to align HTS reads to a reference genome that is organized and indexed using a de Bruijn graph. With its well-handling of repeats, deBGA is substantially faster than state-of-the-art approaches while maintaining similar or higher sensitivity and accuracy. This makes it particularly well-suited to handle the rapidly growing volumes of sequencing data. Furthermore, it provides a promising solution for aligning reads to multiple genomes and graph-based references in HTS applications. AVAILABILITY AND IMPLEMENTATION deBGA is available at https//github.com/hitbc/deBGA CONTACT ydwang@hit.edu.cnSupplementary information Supplementary data are available at Bioinformatics online.
Buscar en Google
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Algoritmos
/
Genoma
/
Secuenciación de Nucleótidos de Alto Rendimiento
Límite:
Animals
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2016
Tipo del documento:
Article
País de afiliación:
China