SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Deriving Group A Streptococcus Typing Information from Short-Read Whole-Genome Sequencing Data

(2014) T. B. T. Athey et al.   JOURNAL OF CLINICAL MICROBIOLOGY

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Rapid bacterial genome sequencing: methods and applications in clinical microbiology

(2013) C. Bertelli et al.   CLINICAL MICROBIOLOGY AND INFECTION

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

(2013) M. T. G. Holden et al.   GENOME RESEARCH

Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing

(2013) A. J. Cody et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Outbreak Investigation Using High-Throughput Genome Sequencing within a Diagnostic Microbiology Laboratory

(2013) N. L. Sherry et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Public Health Genomics and the New Molecular Epidemiology of Bacterial Pathogens

(2013) M.W. Gilmour et al.   Public Health Genomics

Genomic Insights to Control the Emergence of Vancomycin-Resistant Enterococci

(2013) B. P. Howden et al.   mBio

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

(2013) Sandra Reuter et al.   JAMA Internal Medicine

Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory--pipe dream or reality?

(2012) M. E. Torok et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Whole genome sequencing in the prevention and control of Staphylococcus aureus infection

(2012) J.R. Price et al.   JOURNAL OF HOSPITAL INFECTION

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

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

(2012) Chinyere K Okoro et al.   NATURE GENETICS

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

(2012) Kathryn E Holt et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Open-Source Genomic Analysis of Shiga-Toxin–ProducingE. coliO104:H4

(2011) Holger Rohde et al.   NEW ENGLAND JOURNAL OF MEDICINE

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges

(2010) Mark J Pallen et al.   CURRENT OPINION IN MICROBIOLOGY

A Sustained Hospital Outbreak of Vancomycin‐ResistantEnterococcus faeciumBacteremia due to Emergence ofvanB E. faeciumSequence Type 203

(2010) Paul D. R. Johnson et al.   JOURNAL OF INFECTIOUS DISEASES

Bacterial population genomics and infectious disease diagnostics

(2010) Sandeep J. Joseph et al.   TRENDS IN BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Coalescent Simulation of Intracodon Recombination

(2009) M. Arenas et al.   GENETICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH