The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
Genome Biol
; 15(11): 524, 2014.
Article
en En
| MEDLINE
| ID: mdl-25410596
ABSTRACT
Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from http//github.com/marbl/harvest.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Filogenia
/
Bacterias
/
Alineación de Secuencia
/
Genoma Bacteriano
Idioma:
En
Revista:
Genome Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
/
GENETICA
Año:
2014
Tipo del documento:
Article