QUAST: quality assessment tool for genome assemblies

被引:6434
作者
Gurevich, Alexey [1 ]
Saveliev, Vladislav [1 ]
Vyahhi, Nikolay [1 ]
Tesler, Glenn [2 ]
机构
[1] St Petersburg Acad Univ, Russian Acad Sci, Algorithm Biol Lab, St Petersburg 194021, Russia
[2] Univ Calif San Diego, Dept Math, La Jolla, CA 92093 USA
关键词
D O I
10.1093/bioinformatics/btt086
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:1072 / 1075
页数:4
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