Bruce J. Walker

TL;DR: Pilon is a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions, which is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains.

TL;DR: The development of an algorithm for genome assembly, ALLPATHS-LG, and its application to massively parallel DNA sequence data from the human and mouse genomes, generated on the Illumina platform, have good accuracy, short-range contiguity, long-range connectivity, and coverage of the genome.

TL;DR: The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of Diversity in the seed populations that led to each outbreak.

TL;DR: The first whole genome-based analysis of the emergence of drug resistance among clinical isolates of M. tuberculosis shows that the ancestral precursor of the LAM4 XDR outbreak strain in Tugela Ferry gained mutations to first-line drugs at the beginning of the antibiotic era.

TL;DR: By applying a new laboratory design and new assembly algorithm to 16 samples, it is demonstrated that assemblies exceeding finished quality can be obtained from whole-genome shotgun data and automated computation.