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bioRxiv · 10.64898/2026.06.29.735436

Binary search and and set operations on compacted k-mer lists

Dufresne, Y.·Andreace, F.
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Abstract

Sorted lists of elements are particularly good for computing set operations. A single scan of two lists is sufficient to materialize or count the results of the union, intersection, difference, and xor operators. In bioinformatics, only a few tools are designed to perform these operations on k-mers. A fast tool like KMC allows set operations at the cost of storing individual k-mers. In this paper, we introduce a novel way to represent sorted k-mers as a collection of recomposed super-k-mer sorted lists. We introduce the concept of virtual super-k-mer and show how to construct, query and perform set operations on sorted lists of virtual super-k-mers. In the implementation sklib, we demonstrate high throughput of the data structure for construction and set operations, while remaining competitive in query capabilities, within a controlled memory footprint (3.5-4.1x decrease in bits/element compared to KMC).

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Dufresne, Y., Andreace, F.. 2026-07-03. Binary search and and set operations on compacted k-mer lists. https://doi.org/10.64898/2026.06.29.735436

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