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Disk Compression of k-mer Sets

Updated: Nov 24, 2022

WABI Rahman A, Chikhi R, Medvedev P

K-mer based methods have become prevalent in many areas of bioinformatics. In applications such as database search, they often work with large multi-terabyte-sized datasets. Storing such largedatasets is a detriment to tool developers, tool users, and reproducibility efforts. General purposecompressors like gzip, or those designed for read data, are sub-optimal because they do not take intoaccount the specific redundancy pattern in k-mer sets. In our earlier work (Rahman and Medvedev,RECOMB 2020), we presented an algorithm UST-Compress that uses a spectrum-preserving stringset representation to compress a set of k-mers to disk. In this paper, we present two improvedmethods for disk compression of k-mer sets, called ESS-Compress and ESS-Tip-Compress. They use a more relaxed notion of string set representation to further remove redundancy from therepresentation of UST-Compress. We explore their behavior both theoretically and on real data.We show that they improve the compression sizes achieved by UST-Compress by up to 27 percent,across a breadth of datasets. We also derive lower bounds on how well this type of compressionstrategy can hope to do.

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