Genomic technologies have led to tremendous gains in understanding how pathogens
function, evolve and interact. Pathogen diversity is now measurable at high precision and …

Highlights•We describe three long-read sequencing technologies and their
characteristics.•We describe available algorithms for long-read assembly and their …

Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing
become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more …

Streptococcus pneumoniae (pneumococcus) is a major human pathogen producing
structurally diverse capsular polysaccharides. Widespread use of highly successful …

Rapidly decreasing genome sequencing costs have led to a proportionate increase in the
number of samples used in prokaryotic population studies. Extracting single nucleotide …

Genome-wide association studies (GWAS) have become indispensable in human medicine
and genomics, but very few have been carried out on bacteria. Here we introduce Scoary …

Advances in modern sequencing technologies allow us to generate sufficient data to
analyze hundreds of bacterial genomes from a single machine in a single day. This potential …

The emergence of new sequencing technologies has facilitated the use of bacterial whole
genome alignments for evolutionary studies and outbreak analyses. These datasets, of …

Klebsiella pneumoniae has emerged as an important cause of two distinct public health
threats: multi-drug resistant (MDR) healthcare-associated infections and drug susceptible …

Recombination is an important evolutionary force in bacteria, but it remains challenging to
reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present …