QUAST: quality assessment tool for genome assemblies

TLDR

Genome sequencing limitations have produced many assembly algorithms, yet no benchmark exists for evaluating assemblies, especially for previously unsequenced species. This study introduces QUAST, a tool designed to assess and compare genome assemblies. QUAST extends existing comparison software with novel metrics, supports reference‑based and reference‑free evaluation, and generates comprehensive reports, tables, and plots, as demonstrated on three datasets. The resulting tables and plots are provided in the Supplementary Material and as interactive reports on the QUAST website. QUAST is available at http://bioinf.spbau.ru/quast (contact: [e-mail]), and supplementary data can be accessed online via Bioinformatics.

Abstract

Abstract Summary: 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. Availability: http://bioinf.spbau.ru/quast Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.