ntHash2: recursive spaced seed hashing for nucleotide sequences

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 x faster at hashing various spaced seeds than the previous version and 3.8x faster than conventional hashing algorithms with naive 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.

Automated summary

ntHash2 is a fast algorithm for spaced seed hashing that can be integrated into various bioinformatics tools for efficient sequence analysis in genome research. It is faster than previous versions and conventional hashing algorithms, and also improves the uniformity of hash distribution.