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Updated: Aug 31, 2025

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
Published on: July 10, 2020
ntHash2: recursive spaced seed hashing for nucleotide sequences
Parham Kazemi1,2, Johnathan Wong1, Vladimir Nikolić1
1Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
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.
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