PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation

(2016) Brendan R. Jackson et al.   CLINICAL INFECTIOUS DISEASES

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

(2015) Angela J. Taylor et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica

(2014) Pimlapas Leekitcharoenphon et al.   PLoS One

A simple approach to obtain comparable Shigella sonnei MLVA results across laboratories

(2013) Chien-Shun Chiou et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

AGP: A Multimethods Web Server for Alignment-Free Genome Phylogeny

(2013) J. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

(2012) Pimlapas Leekitcharoenphon et al.   BMC GENOMICS

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

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

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

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

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Genetic Relationships of Phage Types and Single Nucleotide Polymorphism Typing of Salmonella enterica Serovar Typhimurium

(2011) S. Pang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Standard operating procedure for computing pangenome trees

(2010) Lars Snipen et al.   Standards in Genomic Sciences

Multilocus variable-number tandem repeat analysis as a molecular tool for subtyping and phylogenetic analysis of bacterial pathogens

(2009) Chien-Shun Chiou   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

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

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