Voyager: rapid taxonomic characterization of long-read mixed-species sequencing samples in sorted motif distance space

Voyager is a novel algorithm that complements real-time sequencing by rapidly mapping long sequencing reads with insertion and deletion errors to a known database of organisms. It utilizes Sorted Motif Distance Space , distances between exact matches of short motifs sorted by rank, to represent sequence similarity in a highly compressed, computationally efficient manner while enabling strain-level discrimination. Voyager incorporates a deconvolution algorithm to discern closely related genomes. It achieves an average species-level accuracy of 99% across 15 datasets, outperforming all evaluated methods. Voyager maintains CPU runtimes comparable to the current fastest methods while using less than half the memory.