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

ABSTRACT:

Motivation

Huge datasets 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 datasets, efficient indexing data structures-that are both scalable and provide rapid query throughput-are paramount.

Results

Here, 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 h. The resulting index takes 142 gigabytes. In comparison, the best competing tools Metagraph and Bifrost were only able to index 11 000 genomes in the same time. In pseudoalignment, these othe

SUBMITTER: Alanko JN 

PROVIDER: S-EPMC10311346 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature