<i>In Silico</i> Evaluation of Variant Calling Methods for Bacterial Whole-Genome Sequencing Assays-Reference-Cited by-同舟云学术

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

Published:2023-07-10 Issue: Volume: Page:
ISSN:0095-1137
Container-title:Journal of Clinical Microbiology
language:en
Short-container-title:J Clin Microbiol

Author:

Seah Yee Mey¹^ORCID,Stewart Mary K.¹,Hoogestraat Daniel¹,Ryder Molly¹,Cookson Brad T.¹²,Salipante Stephen J.¹^ORCID,Hoffman Noah G.¹

Affiliation:

1. Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA

2. Department of Microbiology, University of Washington, Seattle, Washington, USA

Abstract

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.

Publisher

American Society for Microbiology

Subject

Microbiology (medical)

Link

https://journals.asm.org/doi/pdf/10.1128/jcm.01842-22

Reference33 articles.

1. Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

2. Best practices for evaluating single nucleotide variant calling methods for microbial genomics

3. Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP

4. Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

5. Dindel: Accurate indel calls from short-read data

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