Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar

(2017) K A Jolley et al.   Eurosurveillance

Benchmarking of Methods for Genomic Taxonomy

(2014) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica

(2014) Pimlapas Leekitcharoenphon et al.   PLoS One

A pilot study of rapid whole-genome sequencing for the investigation of aLegionellaoutbreak

(2013) Sandra Reuter et al.   BMJ Open

snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

(2012) Pimlapas Leekitcharoenphon et al.   BMC GENOMICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multicenter Evaluation of a Sequence-Based Protocol for Subtyping Shiga Toxins and Standardizing Stx Nomenclature

(2012) F. Scheutz et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

A pilot study of rapid benchtop sequencing ofStaphylococcus aureusandClostridium difficilefor outbreak detection and surveillance

(2012) David W Eyre et al.   BMJ Open

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

(2011) Alexander Mellmann et al.   PLoS One

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION