QUAST: quality assessment tool for genome assemblies

Bioinformatics
Alexey GurevichGlenn Tesler

Abstract

Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website. http://bioinf.spbau.ru/quast . Supplementary data are available at Bioinformatics online.

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Citations

Oct 8, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sergey NurkPavel A Pevzner
May 15, 2013·Bioinformatics·Tanja MagocSteven L Salzberg
Jun 5, 2013·Bioinformatics·Rayan Chikhi, Paul Medvedev
Aug 31, 2013·Bioinformatics·Aleksey V ZiminJames A Yorke
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Jun 3, 2014·BMC Bioinformatics·Sergey KorenAdam M Phillippy
Jun 19, 2014·BMC Research Notes·Vitor C PiroRoberto T Raittz
Jun 17, 2014·Bioinformatics·Andrey D PrjibelskiPavel A Pevzner
Sep 17, 2014·BMC Bioinformatics·Lucian IlieRoberto Solis-Oba
Jun 22, 2014·BMC Bioinformatics·Marten Boetzer, Walter Pirovano
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Jan 17, 2015·Genome Announcements·Vamsi Bharadwaj SvSandhya Mishra
Feb 2, 2016·Nature Methods·Anton Bankevich, Pavel A Pevzner
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