Improving MinHash via the containment index with applications to metagenomic analysis

DOI10.1101/184150zbMATH Open1428.68276OpenAlexW2750898971WikidataQ128306501 ScholiaQ128306501MaRDI QIDQ2011091FDOQ2011091

Authors David Koslicki, Hooman Zabeti 

Publication date 28 November 2019

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

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

zbMATH Keywords

containmentmetagenomicsJaccard indexMinHashtaxonomic classification

Mathematics Subject Classification ID

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

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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

(4)

• Efficient reconciliation of genomic datasets of high similarity
• Estimation of three-way similarities based on connected bit Minwise Hash
• Set similarity search beyond MinHash
• The exact probability law for the approximated similarity from the Minhashing method

Describes a project that uses

Uses Software

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

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