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Article

In Silico Evaluation of Variant Calling Methods for Bacterial Whole-Genome Sequencing Assays.

Journal of clinical microbiology - 23 Aug 2023

Seah Yee Mey, Stewart Mary K, Hoogestraat Daniel, Ryder Molly, Cookson Brad T, Salipante Stephen J, Hoffman Noah G

Abstract excerpt

Identification and analysis of clinically relevant strains of bacteria increasingly relies on whole-genome sequencing. The downstream bioinformatics steps necessary for calling variants from short-read sequences are well-established but seldom validated against haploid genomes. We devised an in silico workflow to introduce single nucleotide polymorphisms (SNP) and indels into bacterial reference genomes, and...

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Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

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Source

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Identifiers

PMID: 37428072
DOI: 10.1128/jcm.01842-22
PMCID: PMC10446864

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 7 Sept 2026. Manifest publication-graph-cohort-2026-09-08.1.

Source receipt: pubmed, retrieved 7 Sept 2026.

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