Improving MinHash via the containment index with applications to metagenomic analysis

DOI10.1101/184150MaRDI QIDQ2011091zbMATH OpenOpenAlexWikidataFDO

Authors David Koslicki, Hooman Zabeti

Publication date 28 November 2019

Published in Applied Mathematics and Computation (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.1101/184150

zbMATH Keywords

containmentJaccard indexmetagenomicsMinHashtaxonomic classification

Mathematics Subject Classification ID

Data structures (68P05) Pattern recognition, speech recognition (68T10) Genetics and epigenetics (92D10)

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Cites work

• scientific article; zbMATH DE number 5763313 (Why is no real title available?)
• Min-wise independent permutations
• Probability and Computing
• Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
• Space/time trade-offs in hash coding with allowable errors

Cited in

(5)

• Set similarity search beyond MinHash
• Estimation of three-way similarities based on connected bit Minwise Hash
• The exact probability law for the approximated similarity from the Minhashing method
• Efficient reconciliation of genomic datasets of high similarity
• Cosine similarity estimation using FracMinHash: theoretical analysis, safety conditions, and implementation

Describes a project that uses

Uses Software

• Mash
• sourmash
• BioBloom Tools
• BLESS
• GemSIM
• HyperLogLog

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