Skip to content
Interactive visualization of assembly graphs
JavaScript Python CSS HTML
Branch: master
Clone or download
Type Name Latest commit message Commit time
Failed to load latest commit information.
agb_src Fix assembly graph filename for SPAdes (issue #2) Jul 23, 2019
conda Update meta.yaml Jan 21, 2019
test_data Update test data Dec 23, 2018
LICENSE Minor fixes in LICENSE and README Nov 30, 2018 Update help Feb 18, 2019 Fix encoding error (issue #3) Jul 23, 2019 Update setup Oct 15, 2018

Assembly Graph Browser (AGB)

Provides interactive visualization of assembly graphs, a wide range of tuning parameters, and various options for modifying/simplifying the graph.


Install conda if you don't have one:

wget -O
bash -b -p ./miniconda
export PATH=$(pwd)/miniconda/bin:$PATH

Create a new conda environment and install AGB into it:

conda create -c almiheenko -c bioconda -n AGB agb

Activate the environment:

source activate AGB


Run AGB to visualize an assembly graph: --graph <GFA(1,2)/FASTG/Graphviz file> -a <assembler_name>

Run AGB on an assembler output folder to visualize an assembly graph with additional useful information. Supported assemblers in this mode: Canu, Flye, SPAdes. -i <assembler_output_dir> -a <assembler_name>

The assembly graph viewer will be saved to agb_output/viewer.html.


Examples of the input data can be found here

You can see AGB examples here


Useful information can be found here


Alla Mikheenko, Mikhail Kolmogorov, "Assembly Graph Browser: interactive visualization of assembly graphs", Bioinformatics. doi: 10.1093/bioinformatics/btz072

You can’t perform that action at this time.