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https://github.com/moshi4/gbkviz

Easy-to-use web application for visualization and comparison of genomes in Genbank file
https://github.com/moshi4/gbkviz

bioinformatics biopython comparative-genomics genbank genomics genomics-visualization microbial-genomics python streamlit visualization webapp

Last synced: 3 months ago
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Easy-to-use web application for visualization and comparison of genomes in Genbank file

Host: GitHub
URL: https://github.com/moshi4/gbkviz
Owner: moshi4
License: mit
Archived: true
Created: 2021-11-12T08:08:11.000Z (about 3 years ago)
Default Branch: main
Last Pushed: 2022-05-27T09:58:50.000Z (over 2 years ago)
Last Synced: 2024-09-27T13:41:13.416Z (3 months ago)
Topics: bioinformatics, biopython, comparative-genomics, genbank, genomics, genomics-visualization, microbial-genomics, python, streamlit, visualization, webapp
Language: Python
Homepage:
Size: 5.25 MB
Stars: 20
Watchers: 2
Forks: 4
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff

Awesome Lists containing this project

README

        # GBKviz: Genbank Data Visualization WebApp

[![Open in Streamlit](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://share.streamlit.io/moshi4/gbkviz/main/src/gbkviz/gbkviz_webapp.py)

![Python3](https://img.shields.io/badge/Language-Python3-steelblue)

![License](https://img.shields.io/badge/License-MIT-steelblue)

[![Latest PyPI version](https://img.shields.io/pypi/v/gbkviz.svg)](https://pypi.python.org/pypi/gbkviz)

[![Bioconda](https://img.shields.io/conda/vn/bioconda/gbkviz.svg?color=green)](https://anaconda.org/bioconda/gbkviz)

[![CI](https://github.com/moshi4/GBKviz/actions/workflows/ci.yml/badge.svg)](https://github.com/moshi4/GBKviz/actions/workflows/ci.yml)

## 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](https://mjsull.github.io/Easyfig/).

![GBKviz Demo GIF](https://raw.githubusercontent.com/moshi4/GBKviz/main/src/gbkviz/gbkviz_demo.gif)  

If you are interested, click [here](https://share.streamlit.io/moshi4/gbkviz/main/src/gbkviz/gbkviz_webapp.py) to try GBKviz on Streamlit Cloud.  

>:warning: 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](https://hub.docker.com/r/moshi4/gbkviz/tags)):**

    docker pull moshi4/gbkviz:latest

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

## Dependencies

- [Streamlit](https://streamlit.io/)  

  Simple web framework for data analysis

- [BioPython](https://github.com/biopython/biopython)  

  Utility tools for computational molecular biology

- [MUMmer](https://github.com/mummer4/mummer)  

  Genome alignment tool for comparative genomics

  

## Command Usage

Launch GBKviz in web browser ():

    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](https://raw.githubusercontent.com/moshi4/GBKviz/main/image/gbkviz_example1.png)  

Fig.1: 4 phage whole genomes comparison result

![GBKviz Example Fig2](https://raw.githubusercontent.com/moshi4/GBKviz/main/image/gbkviz_example2.png)  

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

![GBKviz Example Fig3](https://raw.githubusercontent.com/moshi4/GBKviz/main/image/gbkviz_example3.png)  

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

![GBKviz Example Fig4](https://raw.githubusercontent.com/moshi4/GBKviz/main/image/gbkviz_example4.png)  

Fig.4: Simple CDS visualization with gene label

## Genome Comparison

In GBKviz, [MUMmer](https://github.com/mummer4/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                               |