Mashtree: a rapid comparison of whole genome sequence files

Abstract

In the past decade, the number of publicly available bacterial genomes has increased dramatically. These genomes have been generated for impactful initiatives, especially in the field of genomic epidemiology Genomes are sequenced, shared publicly, and subsequently analyzed for phylogenetic relatedness. If two genomes of epidemiological interest are found to be related, further investigation might be prompted. However, comparing the multitudes of genomes for phylogenetic relatedness is computationally expensive and, with large numbers, laborious. Consequently, there are many strategies to reduce the complexity of the data for downstream analysis, especially using nucleotide stretches of length k (kmers).