Jacqueline A. Keane

TL;DR: Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes, is introduced, making construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results.

TL;DR: Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity.

TL;DR: Roary is introduced, a tool that rapidly builds large-scale pan genomes, identifying the core and dispensable accessory genes and making construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results.

TL;DR: SNPs can be extracted from a 8.3 GB alignment file using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers, and results in multiple formats for downstream analysis are output.

TL;DR: Circlator, the first tool to automate assembly circularization and produce accurate linear representations of circular sequences, correctly circularized 26 of 27 circularizable sequences.