NtHash2: recursive spaced seed hashing for nucleotide sequences.

ABSTRACT:

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

ntHash

SUBMITTER: Kazemi P 

PROVIDER: S-EPMC9563681 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature