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bioRxiv · 10.1101/2022.06.22.497172

KPop: An assembly-free and scalable method for the comparative analysis of microbial genomes

Didelot, X.·Ribeca, P.
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Abstract

The recent explosion in the amount of available sequencing data challenges existing analysis techniques. Here we introduce KPop, a novel versatile method based on full k-mer spectra and dataset-specific transformations, through which thousands of assembled or unassembled microbial genomes can be quickly compared. Unlike minimizer-based methods that produce distances and have lower resolution, KPop is able to accurately map sequences onto a low-dimensional space. Extensive validation on simulated and real-life viral and bacterial datasets shows that KPop can correctly separate sequences at both species and sub-species levels even when the overall genomic diversity is low. KPop also rapidly identifies related sequences and systematically outperforms minimizer-based methods. KPops code is open-source and available on GitHub at https://github.com/PaoloRibeca/KPop.

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Didelot, X., Ribeca, P.. 2022-06-26. KPop: An assembly-free and scalable method for the comparative analysis of microbial genomes. https://doi.org/10.1101/2022.06.22.497172

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