Kmer-db: Instant evolutionary distance estimation

Sebastian Deorowicz; Adam Gudys; MacIej Dlugosz; Marek Kokot; Agnieszka Danek

doi:10.1093/bioinformatics/bty610

Kmer-db: Instant evolutionary distance estimation

Department of Algorithmics and Software (RAU/RAU5)

Research output: Contribution to journal › Article › peer-review

26 Citations (Scopus)

Abstract

Kmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40 715 pathogens in <7 min (on a modern workstation), 26 times faster than Mash, its main competitor. Availability and implementation https://github.com/refresh-bio/kmer-db and http://sun.aei.polsl.pl/REFRESH/kmer-db.

Original language	English
Pages (from-to)	133-136
Number of pages	4
Journal	Bioinformatics
Volume	35
Issue number	1
DOIs	https://doi.org/10.1093/bioinformatics/bty610
Publication status	Published - 1 Jan 2019

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bty610

Cite this

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abstract = "Kmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40 715 pathogens in <7 min (on a modern workstation), 26 times faster than Mash, its main competitor. Availability and implementation https://github.com/refresh-bio/kmer-db and http://sun.aei.polsl.pl/REFRESH/kmer-db.",

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AU - Dlugosz, MacIej

AU - Kokot, Marek

AU - Danek, Agnieszka

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AB - Kmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40 715 pathogens in <7 min (on a modern workstation), 26 times faster than Mash, its main competitor. Availability and implementation https://github.com/refresh-bio/kmer-db and http://sun.aei.polsl.pl/REFRESH/kmer-db.

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Kmer-db: Instant evolutionary distance estimation

Abstract

ASJC Scopus subject areas

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