GBKviz: Genbank Data Visualization WebApp

Overview

GBKviz is a web-based Genbank data visualization tool developed with streamlit web framework. GBKviz allows user to easily and flexibly draw CDSs in specified genomic region. It also supports drawing genome comparison results by MUMmer.

Demo GIF here...

Install

GBKviz is implemented in Python3 (Tested on Ubuntu20.04)

Install PyPI stable version with pip:

pip install gbkviz

If you want to enable genome comparison in GBKviz, MUMmer is required.

Install MUMmer with apt command (Ubuntu):

sudo apt install mummer

Dependencies

• Streamlit
  Web framework for quick development

• BioPython
  Utility tools for computational molecular biology

• MUMmer
  Genome alignment tool for comparative genomics

Command Usage

Launch GBKviz in web browser (http://localhost:8501):

gbkviz_webapp

Usage

SideBar Widgets

• Load example genbank files Checkbox
• Label Checkbox
• ScaleTicks Checkbox
• TopOnly Checkbox
• Feature Label Type Selectbox
• Feature Symbol Selectbox
• Label Angle Selectbox
• ScaleTicks Interval Selectbox
• Label Font Size Numberinput
• ScaleTicks Font Size Numberinput
• Fig Width(cm) Slider
• Fig Track Height(cm) Slider
• Fig Track Size Slider
• Target Feature Types Multiselect
• CDS Colorpicker
• gene Colorpicker
• tRNA Colorpicker
• misc Colorpicker
• Genome Comparison Type Selectbox
• Cross Link (Normal) Colorpicker
• Cross Link (Inverted) Colorpicker