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Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Pightling, Arthur W ; Pettengill, James B ; Wang, Yu ; Rand, Hugh ; Strain, Errol

Genome Biology, 2019-12, Vol.20 (1), p.286-286, Article 286 [Periódico revisado por pares]

England: BioMed Central Ltd

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Título:
Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination
Autor: Pightling, Arthur W ; Pettengill, James B ; Wang, Yu ; Rand, Hugh ; Strain, Errol
Assuntos: Analysis ; Bacterial genetics ; Cluster Analysis ; Contaminants ; Contamination ; Datasets ; DNA Contamination ; DNA sequencing ; E coli ; Escherichia coli ; Escherichia coli - genetics ; Gene mapping ; Genetic aspects ; Genetic polymorphisms ; Genome, Bacterial ; Genomes ; Genomics ; Influence ; Listeria ; Listeria monocytogenes ; Listeria monocytogenes - genetics ; Nucleotide sequence ; Phylogenetics ; Phylogeny ; Salmonella ; Salmonella enterica ; Salmonella enterica - genetics ; Short Report ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Species ; Whole Genome Sequencing
É parte de: Genome Biology, 2019-12, Vol.20 (1), p.286-286, Article 286
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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Descrição: 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.
Editor: England: BioMed Central Ltd
Idioma: Inglês

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Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Pightling, Arthur W ; Pettengill, James B ; Wang, Yu ; Rand, Hugh ; Strain, Errol

England: BioMed Central Ltd

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