gbkviz 1.2.0

Simple web application to visualize and compare genomes in Genbank files

GBKviz: Genbank Data Visualization WebApp

Overview

GBKviz is a web-based Genbank data visualization and comparison tool developed with streamlit web framework. GBKviz allows user to easily and flexibly draw CDSs in user-specified genomic region (PNG or SVG format is available). It also supports drawing genome comparison results by MUMmer. GenomeDiagram, a part of BioPython module, is used to draw the diagram. This software is developed under the strong inspiration of EasyFig.

If you are interested, click here to try GBKviz on Streamlit Cloud.

:warning: Due to the limited resources in Streamlit Cloud, it may be unstable.

Installation

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

GBKviz can also be available with Docker:

docker pull moshi4/gbkviz:latest
docker run -d -p 8501:8501 moshi4/gbkviz:latest

Dependencies

• Streamlit
  Simple web framework for data analysis

• 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

If you are using Docker to start, above command is already executed.

Example

Example of GBKviz genome comparison and visualization results.

Fig.1: 4 phage whole genomes comparison result

Fig.2: 4 E.coli partial genomes comparison result

Fig.3: 4 E.coli whole genomes comparison result

Fig.4: Simple CDS visualization with gene label

Genome Comparison

In GBKviz, MUMmer is used as genome comparison tool.
Following four genome comparison methods are available.

• Nucleotide One-to-One Mapping
• Nucleotide Many-to-Many Mapping
• Protein One-to-One Mapping
• Protein Many-to-Many Mapping

User can download and check genome comparison results file.
Genome comparison results file is in the following tsv format.

Columns	Contents
REF_START	Reference genome alignment start position
REF_END	Reference genome alignment end position
QUERY_START	Query genome alignment start position
QUERY_END	Query genome alignment end position
REF_LENGTH	Reference genome alignment length
QUERY_LENGTH	Query genome alignment length
IDENTITY	Reference and query genome alignment identity (%)
REF_NAME	Reference genome name tag
QUERY_NAME	Query genome name tag