NtHash2: recursive spaced seed hashing for nucleotide sequences.

Abstract

MotivationSpaced seeds are robust alternatives to k-mers in analyzing nucleotide sequences with high base mismatch rates. Hashing is also crucial for efficiently storing abundant sequence data. Here, we introduce ntHash2, a fast algorithm for spaced seed hashing that can be integrated into various bioinformatics tools for efficient sequence analysis with applications in genome research.ResultsntHash2 is up to 2.1× faster at hashing various spaced seeds than the previous version and 3.8× faster than conventional hashing algorithms with naïve adaptation. Additionally, we reduced the collision rate of ntHash for longer k-mer lengths and improved the uniformity of the hash distribution by modifying the canonical hashing mechanism.Availability and implementationntHash2 is freely available online at github.com/bcgsc/ntHash under an MIT license.Supplementary information Supplementary data are available at Bioinformatics online.