Motivation: Spaced 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.
Results: ntHash2 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 implementation: ntHash2 is freely available online at github.com/bcgsc/ntHash under an MIT license.
Supplementary information: Supplementary data are available at Bioinformatics online.
© The Author(s) 2022. Published by Oxford University Press.