Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination.
Genome Biol
; 20(1): 286, 2019 12 18.
Article
em En
| MEDLINE
| ID: mdl-31849328
ABSTRACT
Although it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogenetics, and multi-locus sequencing typing, have not been quantified. By developing and analyzing 720 Listeria monocytogenes, Salmonella enterica, and Escherichia coli short-read datasets, we demonstrate that within-species contamination causes errors that confound clustering analyses, while between-species contamination generally does not. Contaminant reads mapping to references or becoming incorporated into chimeric sequences during assembly are the sources of those errors. Contamination sufficient to influence clustering analyses is present in public sequence databases.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Genoma Bacteriano
/
Contaminação por DNA
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Sequenciamento Completo do Genoma
Idioma:
En
Ano de publicação:
2019
Tipo de documento:
Article