Genomic diversity affects the accuracy of bacterial SNP calling pipelines

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

<br/><strong>Background: </strong>Accurately identifying SNPs from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP...

書目詳細資料
Main Authors:	Bush, S, Foster, D, Eyre, D, Clark, E, De Maio, N, Shaw, L, Stoesser, N, Peto, T, Crook, D, Walker, A
格式:	Journal article
出版:	Oxford University Press 2020

相似書籍

Simulated bacterial genomes for evaluating SNP calling pipelines
由: Bush, S
出版: (2019)

Real sequencing datasets for evaluating bacterial SNP calling pipelines
由: Bush, S
出版: (2019)

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing
由: Sanderson, N, et al.
出版: (2024)

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
由: De Maio, N, et al.
出版: (2019)

Two distinct patterns of Clostridium difficile diversity across Europe indicates contrasting routes of spread
由: Eyre, D, et al.
出版: (2018)

LD-based SNP and genotype calling from next-generation sequencing reads.
由: Menelaou, A
出版: (2012)

Global warming and malaria: a call for accuracy.
由: Reitera, P, et al.
出版: (2004)

Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission.
由: Eyre, D, et al.
出版: (2013)

Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission
由: Eyre, D, et al.
出版: (2013)

Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection
由: Lipworth, S, et al.
出版: (2021)

Exploring uncatalogued genetic variation in antimicrobial resistance gene families in Escherichia coli, an observational analysis
由: Lipworth, S, et al.
出版: (2024)

Risk factors for Klebsiella pneumoniae carbapenemase (KPC) gene acquisition and clinical outcomes across multiple bacterial species
由: Mathers, A, et al.
出版: (2020)

The bacterial sequential Markov coalescent
由: De Maio, N, et al.
出版: (2017)

Multidrug-resistant Escherichia coli soft tissue infection investigated with bacterial whole genome sequencing.
由: Buchanan, R, et al.
出版: (2014)

SNP-o-matic.
由: Manske, H, et al.
出版: (2009)

Risk factors for Clostridium difficile acquisition in infants: importance of study design.
由: Stoesser, N, et al.
出版: (2013)

SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex
由: Lipworth, S, et al.
出版: (2019)

Within-host evolution of bacterial pathogens
由: Didelot, X, et al.
出版: (2016)

Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction
由: Sanderson, N, et al.
出版: (2023)

Pipelining - an approach for machine vision
由: Foster, D, et al.
出版: (1987)

Transforming clinical microbiology with bacterial genome sequencing
由: Didelot, X, et al.
出版: (2012)

Mortality risks associated with empirical antibiotic activity in E. coli bacteraemia: an analysis of electronic health records
由: Yoon, CH, et al.
出版: (2022)

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data
由: Sheppard, A, et al.
出版: (2018)

BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness.
由: Mazariegos-Canellas, O, et al.
出版: (2017)

Comparison of multilocus variable-number tandem-repeat analysis and whole-genome sequencing for investigation of Clostridium difficile transmission.
由: Eyre, D, et al.
出版: (2013)

Cluster effect for SNP–SNP interaction pairs for predicting complex traits
由: Lin, H, et al.
出版: (2024)

High-throughput bacterial SNP typing identifies distinct clusters of SalmonellaTyphi causing typhoid in Nepalese children
由: Holt, K, et al.
出版: (2010)

Transforming clinical microbiology with bacterial genome sequencing.
由: Didelot, X, et al.
出版: (2012)

Flanker: a tool for comparative genomics of gene flanking regions
由: Matlock, W, et al.
出版: (2021)

Control of artefactual variation in reported inter-sample relatedness during clinical use of a Mycobacterium tuberculosis sequencing pipeline
由: Wyllie, D, et al.
出版: (2018)

Increasing incidence of Escherichia coli bacteraemia is driven by an increase in antibiotic-resistant isolates: electronic database study in Oxfordshire 1999-2011.
由: Schlackow, I, et al.
出版: (2012)

Aquatic microenvironments in bacterial ecology and diversity
由: Hunt, Dana E., Ph. D. Massachusetts Institute of Technology
出版: (2008)

The distribution of bacterial doubling times in the wild
由: Gibson, B, et al.
出版: (2018)

Bacterial diversity on different surfaces in urban freshwater
由: Swarup, Sanjay, et al.
出版: (2013)

Machine learning-based pipeline for high accuracy bioparticle sizing
由: Luo, Shaobo, et al.
出版: (2021)

Identifying lineage effects when controlling for population structure improves power in bacterial association studies
由: Earle, S, et al.
出版: (2016)

Clinical Clostridium difficile: clonality and pathogenicity locus diversity.
由: Dingle, K, et al.
出版: (2011)

Relationship between bacterial strain type, host biomarkers, and mortality in Clostridium difficile infection.
由: Walker, A, et al.
出版: (2013)

Evaluation of methods for detecting human reads in microbial sequencing datasets
由: Bush, S, et al.
出版: (2020)

SimBac: simulation of whole bacterial genomes with homologous recombination
由: Didelot, X, et al.
出版: (2015)