February 19, 2013 | Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler
QUAST is a new quality assessment tool for genome assemblies. It improves upon existing assembly comparison software by introducing new metrics and methods. QUAST can evaluate assemblies with or without a reference genome, producing reports, tables, and plots to help scientists assess and compare assemblies. It was used to compare several genome assemblers on three datasets, and its results are available in the Supplementary Material. QUAST is fast and can be run on multi-core processors. It evaluates a wide range of metrics, including contig sizes, misassemblies, structural variations, genome representation, and functional elements. It also introduces new metrics such as NA50 and NGAx, which account for misassemblies. QUAST provides detailed information about each contig, including whether it is unaligned, ambiguously mapped, misassembled, or correct. It also generates visualizations in SVG, PNG, and PDF formats. In a study, QUAST was used to compare assemblies of Escherichia coli, Homo sapiens chromosome 14, and Bombus impatiens. SPAdes and IDBA-UD performed best in most metrics, with SPAdes having a higher NGA50 and genome coverage than IDBA-UD. QUAST helps scientists choose the best assembly software for their research and helps developers improve their algorithms. It is an open-access tool available at http://bioinf.spbau.ru/quast.QUAST is a new quality assessment tool for genome assemblies. It improves upon existing assembly comparison software by introducing new metrics and methods. QUAST can evaluate assemblies with or without a reference genome, producing reports, tables, and plots to help scientists assess and compare assemblies. It was used to compare several genome assemblers on three datasets, and its results are available in the Supplementary Material. QUAST is fast and can be run on multi-core processors. It evaluates a wide range of metrics, including contig sizes, misassemblies, structural variations, genome representation, and functional elements. It also introduces new metrics such as NA50 and NGAx, which account for misassemblies. QUAST provides detailed information about each contig, including whether it is unaligned, ambiguously mapped, misassembled, or correct. It also generates visualizations in SVG, PNG, and PDF formats. In a study, QUAST was used to compare assemblies of Escherichia coli, Homo sapiens chromosome 14, and Bombus impatiens. SPAdes and IDBA-UD performed best in most metrics, with SPAdes having a higher NGA50 and genome coverage than IDBA-UD. QUAST helps scientists choose the best assembly software for their research and helps developers improve their algorithms. It is an open-access tool available at http://bioinf.spbau.ru/quast.