title: QUAST: quality assessment tool for genome assemblies.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  http://bioinf.spbau.ru/quast .
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia. gurevich@bioinf.spbau.ru
authors: Alexey
authors: A
authors: Gurevich
authors: Vladislav
authors: V
authors: Saveliev
authors: Nikolay
authors: N
authors: Vyahhi
authors: Glenn
authors: G
authors: Tesler
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping; D020451:Contig Mapping; D004926:Escherichia coli / Q000235:genetics; D016678:Genome; D056914:Genomic Structural Variation; D023281:Genomics / Q000592:standards*; D006801:Humans; D011786:Quality Control; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000592:standards*; D012984:Software