Assembly Graph Browser (AGB)

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

Installation

Install conda if you don't have one:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p ./miniconda
unset PYTHONPATH
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

Usage

Run AGB to visualize an assembly graph:

    agb.py --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.

    agb.py -i <assembler_output_dir> -a <assembler_name>

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

Examples

Examples of the input data can be found here https://github.com/almiheenko/AGB/tree/master/test_data

You can see AGB examples here https://almiheenko.github.io/AGB/index.html

Manual

Useful information can be found here https://almiheenko.github.io/AGB/manual.html

Citation

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