Summary
The Graphical Fragment Assembly (GFA) formats are emerging standard formats for the representation of sequence graphs. While GFA 1 was primarely targeting assembly graphs, the newer GFA 2 format introduces several features, which makes it suitable for representing other kinds of information, such as scaffolding graphs, variation graphs, alignment graphs, and colored metagenomic graphs. Here, we present GfaViz, an interactive graphical tool for the visualization of sequence graphs in GFA format. The software supports all new features of GFA 2 and introduces conventions for their visualization. The user can choose between two different layouts and multiple styles for representing single elements or groups. All customizations can be stored in custom tags of the GFA format itself, without requiring external configuration files. Stylesheets are supported for storing standard configuration options for groups of files. The visualizations can be exported to raster and vector graphics formats. A command line interface allows for batch generation of images.
Availability and Implementation
GfaViz is available at https://github.com/ggonnella/gfaviz.
Supplementary information
Supplementary data are available at Bioinformatics online.
[1]
Justin Zobel,et al.
Bandage: interactive visualization of de novo genome assemblies
,
2015,
bioRxiv.
[2]
M. Schatz,et al.
Algorithms Gage: a Critical Evaluation of Genome Assemblies and Assembly Material Supplemental
,
2008
.
[3]
Michael Jünger,et al.
Drawing Large Graphs with a Potential-Field-Based Multilevel Algorithm
,
2004,
GD.
[4]
Stefan Kurtz,et al.
GfaPy: a flexible and extensible software library for handling sequence graphs in Python
,
2017,
Bioinform..
[5]
Yehuda Koren,et al.
Graph Drawing by Stress Majorization
,
2004,
GD.
[6]
William Jones,et al.
Variation graph toolkit improves read mapping by representing genetic variation in the reference
,
2018,
Nature Biotechnology.