Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.14.382713v1?rss=1

Authors: Shibuya, Y., Kucherov, G.

Abstract:

Motivation: In many bioinformatics pipelines, k-mer counting is often a required step, with existing methods focusing on optimizing time or memory usage. These methods usually produce very large count tables explicitly representing k-mers themselves. Solutions avoiding explicit representation of k-mers include Minimal Perfect Hash Functions (MPHFs) or Count-Min sketches. The former is only applicable to static maps not subject to updates, while the latter suffers from potentially very large point-query errors, making it unsuitable when counters are required to be highly accurate. Results: We introduce Set-Min sketch, a sketching technique inspired by Count-Min sketch, for representing associative maps, more specifically, k-mer count tables. We show that Set-Min sketch provides a very low error rate, both in terms of the probability and the size of errors, much lower than a Count-Min sketch of similar dimensions. On the other hand, Set-Min sketches are shown to take up to an order of magnitude less space than MPHF-based solutions, especially for large values of k. Space-efficiency of Set-min takes advantage of the power-law distribution of k-mer counts in genomic datasets.

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