Gen2Epi: an automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae

Genomic epidemiology and population structure of Neisseria gonorrhoeae from remote highly endemic Western Australian populations

(2018) Barakat A. Al Suwayyid et al.   BMC GENOMICS

Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey

(2018) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand

(2017) Robyn S Lee et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

(2017) W. Demczuk et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny

(2017) Alan K. L. Tsang et al.   Scientific Reports

Neisseria genomics: current status and future perspectives

(2017) Odile B Harrison et al.   Pathogens and Disease

Genomic sequencing of Neisseria gonorrhoeae to respond to the urgent threat of antimicrobial-resistant gonorrhea

(2017) A. Jeanine Abrams et al.   Pathogens and Disease

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

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

The novel 2016 WHONeisseria gonorrhoeaereference strains for global quality assurance of laboratory investigations: phenotypic, genetic and reference genome characterization

(2016) Magnus Unemo et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genomic Epidemiology and Molecular Resistance Mechanisms of Azithromycin-Resistant Neisseria gonorrhoeae in Canada from 1997 to 2014

(2016) Walter Demczuk et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Population structure ofNeisseria gonorrhoeaebased on whole genome data and its relationship with antibiotic resistance

(2015) Matthew N. Ezewudo et al.   PeerJ

Ragout--a reference-assisted assembly tool for bacterial genomes

(2014) M. Kolmogorov et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

(2014) Walter Demczuk et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Using Crude Whole-Genome Assemblies of Neisseria gonorrhoeae as a Platform for Strain Analysis: Clonal Spread of Gonorrhea Infection in Saskatchewan, Canada

(2014) S. Vidovic et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

Short read sequence typing (SRST): multi-locus sequence types from short reads

(2012) Michael Inouye 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The challenges of sequencing by synthesis

(2009) Carl W Fuller et al.   NATURE BIOTECHNOLOGY

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

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

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