Effective parallel multicore-optimized k-mers counting algorithm

DOI10.1007/978-3-662-49192-8_38MaRDI QIDQ2794384zbMATH OpenOpenAlexFDO

Authors Tomáš Farkaš, Peter Kubán, Maria Lucka

Publication date 10 March 2016

Published in Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-662-49192-8_38

zbMATH Keywords

\(k\)-mers countingbucket sortgenome assemblyparallel computationsorting

Mathematics Subject Classification ID

Searching and sorting (68P10) Parallel algorithms in computer science (68W10) Algorithms on strings (68W32) Protein sequences, DNA sequences (92D20)

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• scientific article; zbMATH DE number 1830949

Cited in

(6)

• Fast approximation of frequent \(k\)-mers and applications to metagenomics
• Robust k-mer frequency estimation using gapped k-mers
• A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets
• Space-Efficient Representation of Genomic k-Mer Count Tables
• Accurate k-mer classification using read profiles
• Fast gapped k-mer counting with subdivided multi-way bucketed cuckoo hash tables

Describes a project that uses

Uses Software

• OpenMPI
• KMC
• KAnalyze
• Turtle

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