Tag: Hashing

ntHash 2.0.0 – Recursive Nucleotide Hashing

ntHash 2.0.0

:: DESCRIPTION

ntHash is a hashing algorithm tuned for processing DNA/RNA sequences. It performs the best when calculating hash values for adjacent k-mers in an input sequence, operating an order of magnitude faster than the nearest competitors in typical use cases.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ntHash

:: MORE INFORMATION

Citation

ntHash: recursive nucleotide hashing.
Mohamadi H, Chu J, Vandervalk BP, Birol I.
Bioinformatics. 2016 Jul 16. pii: btw397.

ISSH – Iterative Spaced Seed Hashing

ISSH

:: DESCRIPTION

ISSH is an iterative algorithm that combines multiple spaced seed hashes by exploiting the similarity of adjacent hash values in order to efficiently compute the next hash.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ISSH

:: MORE INFORMATION

Citation

E.Petrucci, L.Noé, C. Pizzi, M. Comin
Iterative Spaced Seed Hashing: Closing the gap between spaced seed hashing and k-mer hashing
In Proceedings of the 15th International Symposium on Bioinformatics Research and Applications, pp. 208-219.

FISH – Fast Indexing for Spaced-seed Hashing

FISH

:: DESCRIPTION

FISH is a novel algorithm,which based on the indexing of small blocks that can be combined to obtain the hashing of spaced-seeds of any length. The method exploits the fast computation of the hashing of runs of consecutive 1 in the spaced seeds, that basically correspond to k-mer of the length of the run.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FISH

:: MORE INFORMATION

Citation

BMC Bioinformatics, 19 (Suppl 15), 441 2018 Nov 30
Efficient Computation of Spaced Seed Hashing With Block Indexing
Samuele Girotto , Matteo Comin , Cinzia Pizzi

FSH – Fast Spaced Seed Hashing

FSH

:: DESCRIPTION

FSH exploits the similarity of adjacent spaced seed hash values in an input sequence in order to efficiently compute the next hash.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FSH

:: MORE INFORMATION

Citation

J Comput Biol 2019 Dec 4
Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing
Enrico Petrucci , Laurent Noé , Cinzia Pizzi , Matteo Comin