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. 2023 Jul 5;51(W1):W601-W606.
doi: 10.1093/nar/gkad406.

WebQUAST: online evaluation of genome assemblies

Alla Mikheenko  1 , Vladislav Saveliev  2   3 , Pascal Hirsch  4 , Alexey Gurevich  5   6
Affiliations

WebQUAST: online evaluation of genome assemblies

Alla Mikheenko et al. Nucleic Acids Res. .

Abstract

Selecting proper genome assembly is key for downstream analysis in genomics studies. However, the availability of many genome assembly tools and the huge variety of their running parameters challenge this task. The existing online evaluation tools are limited to specific taxa or provide just a one-sided view on the assembly quality. We present WebQUAST, a web server for multifaceted quality assessment and comparison of genome assemblies based on the state-of-the-art QUAST tool. The server is freely available at https://www.ccb.uni-saarland.de/quast/. WebQUAST can handle an unlimited number of genome assemblies and evaluate them against a user-provided or pre-loaded reference genome or in a completely reference-free fashion. We demonstrate key WebQUAST features in three common evaluation scenarios: assembly of an unknown species, a model organism, and a close variant of it.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
WebQUAST text reports for E. coli assemblies in the (A) reference-free and (B) reference-based evaluation mode. Unless otherwise noted, all statistics are based on contigs of size ≥ 500 bp (the default cut-off). Heatmap highlights the best value in each row which could be the largest or the smallest number depending on the quality metric. Heatmap is not used for # contigs and GC (%) due to the ambiguity of these metrics trends.
Figure 2.
Figure 2.
Icarus viewers for E. coli assemblies aligned against (A) the reference genome matching the dataset and (B) a close reference. The reference regions between 0.5 Mb and 0.7 Mb are shown. mis: X + Y stands for the total number of extensive (X) and local (Y) misassemblies per assembly. Correctly assembled contigs are colored green and aquamarine (if longer than 10 kb and similar in at least three assemblies), and fragments of misassembled contigs are colored pink and orange (if similar in at least three assemblies). Red triangles designate the sides of alignment breakpoints for misassembled contigs. Contig names are shown for contigs of sufficient size.
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