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Easy-to-use web application for visualization and comparison of genomes in Genbank file

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GBKviz: Genbank Data Visualization WebApp

Open in Streamlit Python3 License Latest PyPI version Bioconda CI

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.

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

⚠️ Due to the limited resources in Streamlit Cloud, it may be unstable. When performing comparative analysis of users' genomic data, use the stable, locally installed version.

Installation

GBKviz is implemented in Python3. MUMmer is required for genome comparison.

Install bioconda package:

conda install -c bioconda -c conda-forge gbkviz

Install PyPI package:

pip install gbkviz

Use Docker (Docker Image):

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.

GBKviz Example Fig1
Fig.1: 4 phage whole genomes comparison result

GBKviz Example Fig2
Fig.2: 4 E.coli partial genomes comparison result

GBKviz Example Fig3
Fig.3: 4 E.coli whole genomes comparison result

GBKviz Example Fig4
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