Sparse and skew hashing of K-mers.

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 . 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.Availability and implementation https://github.com/jermp/sshash.Supplementary information Supplementary data are available at Bioinformatics online.