SnapperDB: a database solution for routine sequencing analysis of bacterial isolates

An outbreak of Shiga toxin-producing Escherichia coli serogroup O157 linked to a lamb-feeding event

(2016) S. ROWELL et al.   EPIDEMIOLOGY AND INFECTION

Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis

(2016) T. INNS et al.   EPIDEMIOLOGY AND INFECTION

Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study

(2016) Louise J Pankhurst et al.   Lancet Respiratory Medicine

Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress

(2015) Claire Jenkins et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS