Assembly Graph Browser: Interactive visualization of assembly graphs

Abstract

Currently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Browser (AGB) tool that visualizes large assembly graphs, extending the functionality of previously developed visualization approaches. Assembly Graph Browser includes a number of novel functions including repeat analysis, construction of the contracted assembly graphs (i.e. the graphs obtained by collapsing a selected set of edges) and a new approach to visualizing large assembly graphs. Availability and implementation: http://www.github.com/almiheenko/AGB. Supplementary information: Supplementary data are available at Bioinformatics online.