Sparse and Skew Hashing of K-Mers

Pibiri, G. E.

doi:10.1101/2022.01.15.476199

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bioRxiv · 10.1101/2022.01.15.476199

Sparse and Skew Hashing of K-Mers

Pibiri, G. E.

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Abstract

MotivationA dictionary of k-mers is a data structure that stores a set of n distinct k-mers and supports membership queries. This data structure is at the hearth of many important tasks in computational biology. High-throughput sequencing of DNA can produce very large k-mer sets, in the size of billions of strings - in such cases, the memory consumption and query efficiency of the data structure is a concrete challenge. ResultsTo tackle this problem, we describe a compressed and associative dictionary for k-mers, that is: a data structure where strings are represented in compact form and each of them is associated to a unique integer identifier in the range [0, n). We show that some statistical properties of k-mer minimizers can be exploited by minimal perfect hashing to substantially improve the space/time trade-off of the dictionary compared to the best-known solutions. AvailabilityThe C++ implementation of the dictionary is available at https://github.com/jermp/sshash. Contactgiulio.ermanno.pibiri@isti.cnr.it

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Pibiri, G. E.. 2022-01-18. Sparse and Skew Hashing of K-Mers. https://doi.org/10.1101/2022.01.15.476199

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