Article

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

2024-03-16

Abstract excerpt

Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, the construction of phylogenetic trees, and antimicrobial resistance prediction. This study presents a comprehensive benchmarking of SNP and indel variant calling accuracy across 14 diverse bacterial species using Oxford Nanopore Technologies (ONT) and Illumina sequencing. We generate gold standa...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 0fd12125-4512-5c75-be61-27a463162d26
DOI: 10.1101/2024.03.15.585313

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence dataDOI 10.1101/2024.03.15.585313Read

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

Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogensSemantic proximity Read

Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Semantic proximity Read

A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.Semantic proximity Read

Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens.Semantic proximity Read

miniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data.Semantic proximity Read

Fast and accurate variant identification tool for sequencing-based studies.Semantic proximity Read

Generalizable characteristics of false-positive bacterial variant calls.Semantic proximity Read

Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing.Semantic proximity Read

Accelerated and High-Accuracy Variant Calling on Oxford Nanopore Technologies Sequencing Data with the Sentieon DNAscope LongRead and Hybrid PipelinesSemantic proximity Read

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

Creating a universal SNP and small indel variant caller with deep neural networksSemantic proximity Read