Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.

ABSTRACT:

Motivation

The Jaccard similarity on k-mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations, tools such as MashMap can scale to massive numbers of pairwise comparisons while still providing useful similarity estimates. However, due to their reliance on minimizer winnowing, previous versions of MashMap were shown to be biased and inconsistent estimators of Jaccard similarity. This directly impacts downstream tools that rely on the accuracy of these estimates.

Results

To address this, we propose the minmer winnowing scheme, which generalizes the minimizer scheme by use of a rolling minhash with multiple sampled k-mers per window. We show both theoretically and empirically t

SUBMITTER: Kille B 

PROVIDER: S-EPMC10505501 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature