Hierarchically Visualizing Metagenome Assembly Graphs with MetagenomeScope

Manual inspection of sequence assembly graphs can be useful not only as a debugging tool when developing assembly software, but also as a way to uncover interesting biological patterns, such as structural differences between the two or more haplotypes being analyzed in a genomic or metagenomic experiment. Current tools for visualizing these graphs, however, emphasize a high-level representation, based on force-directed layouts, aimed at revealing the broad level quality of an assembly rather than its small scale structure. As a result, it is difficult for users to piece together a unified understanding of both the high-level structure of the assembly graph and the detailed patterns found within these graphs. We present a new strategy for displaying genome assembly graphs that emphasizes the expected linear structure of genome assemblies and allows a multi-level exploration of the structure of the graph. This approach is implemented in MetagenomeScope, an interactive web-based tool. We detail the novel layout algorithm employed byMetagenomeScope and provide a qualitative comparison with the main tools currently used to explore genome assembly graphs. We demonstrate that MetagenomeScope provides a set of unique capabilities that enable the effective visual exploration of assembly graphs in the context of several common workflows, such as genome finishing or the discovery of structural variants within assemblies.