Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation

Air-conditioner cooling towers as complex reservoirs and continuous source of Legionella pneumophila infection evidenced by a genomic analysis study in 2017, Switzerland

(2019) Daniel Wüthrich et al.   Eurosurveillance

Next-generation sequencing technologies and their application to the study and control of bacterial infections

(2018) J. Besser et al.   CLINICAL MICROBIOLOGY AND INFECTION

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches

(2018) A.C. Schürch et al.   CLINICAL MICROBIOLOGY AND INFECTION

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology

(2018) J.W.A. Rossen et al.   CLINICAL MICROBIOLOGY AND INFECTION

A primer on microbial bioinformatics for nonbioinformaticians

(2018) J.A. Carriço et al.   CLINICAL MICROBIOLOGY AND INFECTION

Outbreak of vancomycin-resistant Enterococcus faecium clone ST796, Switzerland, December 2017 to April 2018

(2018) Nasstasja Wassilew et al.   Eurosurveillance

Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak

(2018) Madison E. Pearce et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory

(2018) Anamaria Crisan et al.   PeerJ

Vancomycin-resistant Enterococcus faecium sequence type 796 - rapid international dissemination of a new epidemic clone

(2018) Andrew A. Mahony et al.   Antimicrobial Resistance and Infection Control

From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

(2018) Francois Balloux et al.   TRENDS IN MICROBIOLOGY

Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

(2018) Stephen Bruinsma et al.   BMC GENOMICS

Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review

(2017) F. Tagini et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Application of next generation sequencing in clinical microbiology and infection prevention

(2017) Ruud H. Deurenberg et al.   JOURNAL OF BIOTECHNOLOGY

Reference standards for next-generation sequencing

(2017) Simon A. Hardwick et al.   NATURE REVIEWS GENETICS

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Evolutionary origins of the emergent ST796 clone of vancomycin resistantEnterococcus faecium

(2017) Andrew H. Buultjens et al.   PeerJ

Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories

(2016) Amy S. Gargis et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis

(2016) Andrea D. Tyler et al.   PLoS One

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Impact of three Illumina library construction methods on GC bias and HLA genotype calling

(2015) James H. Lan et al.   HUMAN IMMUNOLOGY

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

(2015) Mark de Been et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

MLST revisited: the gene-by-gene approach to bacterial genomics

(2013) Martin C. J. Maiden et al.   NATURE REVIEWS MICROBIOLOGY

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

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

(2012) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS