The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data

(2015) Shaokang Zhang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

Multi-laboratory evaluation of the rapid genoserotyping array (SGSA) for the identification of Salmonella serovars

(2014) Catherine Yoshida et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

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

(2014) Michael Inouye et al.   Genome Medicine

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh 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

Public Health Genomics and the New Molecular Epidemiology of Bacterial Pathogens

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

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory

(2012) W. M. Dunne et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

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

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

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

(2012) K. A. Jolley et al.   MICROBIOLOGY-SGM

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter

(2012) Samuel K. Sheppard et al.   Genes

Rapid Genoserotyping Tool for Classification of Salmonella Serovars

(2011) K. Franklin et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Everything at once: Comparative analysis of the genomes of bacterial pathogens

(2011) Chad R. Laing et al.   VETERINARY MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Development of a Multiplex Primer Extension Assay for Rapid Detection of Salmonella Isolates of Diverse Serotypes

(2010) E. Ben-Darif et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Molecular Determination of H Antigens of Salmonella by Use of a Microsphere-Based Liquid Array

(2010) J. R. McQuiston et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Development and Evaluation of a Multiplex Real-Time Polymerase Chain Reaction Procedure to Clinically Type Prevalent Salmonella enterica Serovars

(2010) Nélida Muñoz et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Evaluation of the Premi®Test Salmonella, a commercial low-density DNA microarray system intended for routine identification and typing of Salmonella enterica

(2008) Pierre Wattiau et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Development of an oligonucleotide microarray method forSalmonellaserotyping

(2008) B. Tankouo-Sandjong et al.   Microbial Biotechnology