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

Katedra Algorytmiki i Oprogramowania (RAU/RAU5)

Wyniki badań: Wkład do czasopisma › Artykuł › recenzja

26 Cytowania z bazy Scopus

Abstrakt

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.

Język oryginału	angielski
Strony (od–do)	133-136
Liczba stron	4
Czasopismo	Bioinformatics
Tom	35
Numer wydania	1
Identyfikatory DOI	https://doi.org/10.1093/bioinformatics/bty610
Status publikacji	Opublikowano - 1 sty 2019

Obszary tematyczne ASJC Scopus

Statystyka i prawdopodobieństwo
Biochemia
Biologia molekularna
Zastosowania informatyki
Teoria i matematyka obliczeń
Matematyka obliczeniowa

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10.1093/bioinformatics/bty610

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Cytowanie

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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.",

author = "Sebastian Deorowicz and Adam Gudys and MacIej Dlugosz and Marek Kokot and Agnieszka Danek",

year = "2019",

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doi = "10.1093/bioinformatics/bty610",

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T2 - Instant evolutionary distance estimation

AU - Deorowicz, Sebastian

AU - Gudys, Adam

AU - Dlugosz, MacIej

AU - Kokot, Marek

AU - Danek, Agnieszka

PY - 2019/1/1

Y1 - 2019/1/1

N2 - 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.

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.

UR - https://www.scopus.com/pages/publications/85058769623

U2 - 10.1093/bioinformatics/bty610

DO - 10.1093/bioinformatics/bty610

M3 - Article

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JO - Bioinformatics

JF - Bioinformatics

IS - 1

ER -

Kmer-db: Instant evolutionary distance estimation

Abstrakt

Obszary tematyczne ASJC Scopus

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