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Article

Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data.

eLife - 10 Oct 2024

Hall Michael B, Wick Ryan R, Judd Louise M, Nguyen An N, Steinig Eike J, Xie Ouli, Davies Mark, Seemann Torsten, Stinear Timothy P, Coin Lachlan

Abstract excerpt

Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, the construction of phylogenetic trees, and antimicrobial resistance detection. This study presents a comprehensive benchmarking of variant calling accuracy in bacterial genomes using Oxford Nanopore Technologies (ONT) sequencing data. We evaluated three ONT basecalling models and both simplex...

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Identifiers

PMID: 39388235
DOI: 10.7554/eLife.98300
PMCID: PMC11466455

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