Assembly Graph Browser: interactive visualization of assembly graphs

Alla Mikheenko; Mikhail Kolmogorov

doi:10.1093/bioinformatics/btz072

Assembly Graph Browser: interactive visualization of assembly graphs

Bioinformatics. 2019 Sep 15;35(18):3476-3478. doi: 10.1093/bioinformatics/btz072.

Authors

Alla Mikheenko¹, Mikhail Kolmogorov²

Affiliations

¹ Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia.
² Department of Computer Science and Engineering, University of California, San Diego, CA, USA.

PMID: 30715194
DOI: 10.1093/bioinformatics/btz072

Abstract

Summary: 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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Software*