Snipe: highly sensitive pathogen detection from metagenomic sequencing data.
Brief Bioinform
; 22(5)2021 09 02.
Article
em En
| MEDLINE
| ID: mdl-33822895
ABSTRACT
Metagenomics data provide rich information for the detection of foodborne pathogens from food and environmental samples that are mixed with complex background bacteria strains. While pathogen detection from metagenomic sequencing data has become an activity of increasing interest, shotgun sequencing of uncultured food samples typically produces data that contain reads from many different organisms, making accurate strain typing a challenging task. Particularly, as many pathogens may contain a common set of genes that are highly similar to those from normal bacteria in food samples, traditional strain-level abundance profiling approaches do not perform well at detecting pathogens of very low abundance levels. To overcome this limitation, we propose an abundance correction method based on species-specific genomic regions to achieve high sensitivity and high specificity in target pathogen detection at low abundance.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Bactérias
/
Infecções Bacterianas
/
Metagenoma
/
Metagenômica
/
Sequenciamento de Nucleotídeos em Larga Escala
/
Doenças Transmitidas por Alimentos
/
Sequenciamento Completo do Genoma
Tipo de estudo:
Diagnostic_studies
/
Evaluation_studies
/
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Brief Bioinform
Assunto da revista:
BIOLOGIA
/
INFORMATICA MEDICA
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
China