Gclust: A Parallel Clustering Tool for Microbial Genomic Data.
Genomics Proteomics Bioinformatics
; 17(5): 496-502, 2019 10.
Article
em En
| MEDLINE
| ID: mdl-31917259
ABSTRACT
The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources. Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering analysis is essential. However, existing clustering algorithms perform poorly on long genomic sequences. In this article, we present Gclust, a parallel program for clustering complete or draft genomic sequences, where clustering is accelerated with a novel parallelization strategy and a fast sequence comparison algorithm using sparse suffix arrays (SSAs). Moreover, genome identity measures between two sequences are calculated based on their maximal exact matches (MEMs). In this paper, we demonstrate the high speed and clustering quality of Gclust by examining four genome sequence datasets. Gclust is freely available for non-commercial use at https//github.com/niu-lab/gclust. We also introduce a web server for clustering user-uploaded genomes at http//niulab.scgrid.cn/gclust.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Interface Usuário-Computador
/
Genoma
Idioma:
En
Revista:
Genomics Proteomics Bioinformatics
Ano de publicação:
2019
Tipo de documento:
Article