QUAST: quality assessment tool for genome assemblies

QUAST: quality assessment tool for genome assemblies

Advance Access publication February 19, 2013 | Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler
The article introduces QUAST, a quality assessment tool for evaluating and comparing genome assemblies. QUAST addresses the limitations of existing assembly algorithms and methods for comparing assemblers, which often lack a recognized benchmark and are not suitable for evaluating assemblies of previously unsequenced species. QUAST can evaluate assemblies with or without a reference genome, producing detailed reports, summary tables, and plots to aid researchers in their work. The tool includes a range of metrics, such as contig sizes, misassemblies, structural variations, and genome representation, and it is designed to be user-friendly and efficient, with parallelized steps for multi-core processors. The authors demonstrate QUAST's effectiveness by comparing several genome assemblers on three datasets: *Escherichia coli*, *Homo sapiens chromosome 14*, and *Bombus impatiens*. The results show that SPAdes and IDBA-UD perform well in most metrics, with SPAdes having a larger NG50 and assembling a higher percentage of the genome, while IDBA-UD assembles the largest contig. QUAST is available at http://bioinf.spbau.ru/quast.The article introduces QUAST, a quality assessment tool for evaluating and comparing genome assemblies. QUAST addresses the limitations of existing assembly algorithms and methods for comparing assemblers, which often lack a recognized benchmark and are not suitable for evaluating assemblies of previously unsequenced species. QUAST can evaluate assemblies with or without a reference genome, producing detailed reports, summary tables, and plots to aid researchers in their work. The tool includes a range of metrics, such as contig sizes, misassemblies, structural variations, and genome representation, and it is designed to be user-friendly and efficient, with parallelized steps for multi-core processors. The authors demonstrate QUAST's effectiveness by comparing several genome assemblers on three datasets: *Escherichia coli*, *Homo sapiens chromosome 14*, and *Bombus impatiens*. The results show that SPAdes and IDBA-UD perform well in most metrics, with SPAdes having a larger NG50 and assembling a higher percentage of the genome, while IDBA-UD assembles the largest contig. QUAST is available at http://bioinf.spbau.ru/quast.
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