Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes

Abstract

MotivationHuge data sets containing whole-genome sequences of bacterial strains are now commonplace and represent a rich and important resource for modern genomic epidemiology and metagenomics. In order to efficiently make use of these data sets, efficient indexing data structures -- that are both scalable and provide rapid query throughput -- are paramount. ResultsHere, we present Themisto, a scalable colored k-mer index designed for large collections of microbial reference genomes, that works for both short and long read data. Themisto indexes 179 thousand Salmonella enterica genomes in 9 hours. The resulting index takes 142 gigabytes. In comparison, the best competing tools Metagraph and Bifrost were only able to index 11 thousand genomes in the same time. In pseudoalignment, these other tools were either an order of magnitude slower than Themisto, or used an order of magnitude more memory. Themisto also offers superior pseudoalignment quality, achieving a higher recall than previous methods on Nanopore read sets. Availability and implementationThemisto is available and documented as a C++ package at https://github.com/algbio/themisto available under the GPLv2 license. Contactjarno.alanko@helsinki.fi Supplementary informationSupplementary data are available at Bioinformatics online.