pubmed.ncbi.nlm.nih.gov

QUAST: quality assessment tool for genome assemblies - PubMed

  • ️Tue Jan 01 2013

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al. Bioinformatics. 2013.

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 .

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.

Alignment of single-cell E.coli assemblies to the reference genome. On all tracks, the x-axis is genome position. Top track: Read coverage on a logarithmic scale. The red curve shows coverage binned in 1000 bp windows. Blue positions on the x-axis have zero coverage, even if their bin has some coverage. Coverage is highly non-uniform, ranging from 0 to near 10 000. All other tracks: Comparison of positions of aligned contigs. Contigs that align correctly are coloured blue if the boundaries agree (within 2000 bp on each side) in at least half of the assemblies, and green otherwise. Contigs with misassemblies are broken into blocks and coloured orange if the boundaries agree in at least half of the assemblies, and red otherwise. Contigs are staggered vertically and are shown in different shades of their colour to distinguish the separate contigs, including small ones

Similar articles

Cited by

References

    1. Bankevich A, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012;19:455–477. - PMC - PubMed
    1. Barthelson R, et al. Plantagora: modeling whole genome sequencing and assembly of plant genomes. PLoS One. 2011;6:e28436. - PMC - PubMed
    1. Blattner FR, et al. The complete genome sequence of Escherichia coli K-12. Science. 1997;277:1453–1462. - PubMed
    1. Bohlin J, et al. Analysis of intra-genomic GC content homogeneity within prokaryotes. BMC Genomics. 2010;11:464. - PMC - PubMed
    1. Chitsaz H, et al. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat. Biotechnol. 2011;29:915–921. - PMC - PubMed

Publication types

MeSH terms