pgv-gui

pgv-gui command is used to launch the pyGenomeViz Web Application. It is developed with the streamlit web application framework, and users can easily visualize the genomic features of Genbank files and their comparison results with GUI.

pyGenomeViz web application example (Demo Page)

Installation

Additional installation of streamlit is required. BLAST, MUMmer, MMseqs are also required to enable the genome comparison functionality.

Conda

conda install -c conda-forge -c bioconda pygenomeviz streamlit blast mummer mmseqs2

Pip

pip install pygenomeviz[gui]

On Ubuntu22.04 or later, BLAST, MUMmer, MMseqs can be installed with apt command.

sudo apt install ncbi-blast+ mummer mmseqs2

Docker

docker run -it --rm -p 8501:8501 ghcr.io/moshi4/pygenomeviz:latest pgv-gui

Usage

$ pgv-gui --help
usage: pgv-gui [options]

pyGenomeViz CLI for launching Streamlit Web Application

Users can access the web app with http://localhost:8501 (default).

optional arguments:
  -p , --port    Port number to open web browser (Default: 8501)
  -v, --version  Print version information
  -h, --help     Show this help message and exit

Info

By uploading a user Genbank file with a browser, a visualization figure of each genomic feature is automatically displayed. By setting each widget value, user can interactively change the appearance of the figure, genome comparison method, etc.