{"id":15176729,"url":"https://github.com/moshi4/gbkviz","last_synced_at":"2025-10-01T16:30:37.225Z","repository":{"id":41448695,"uuid":"427280071","full_name":"moshi4/GBKviz","owner":"moshi4","description":"Easy-to-use web application for visualization and comparison of genomes in Genbank file","archived":true,"fork":false,"pushed_at":"2022-05-27T09:58:50.000Z","size":5509,"stargazers_count":21,"open_issues_count":0,"forks_count":4,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-01-16T07:56:19.623Z","etag":null,"topics":["bioinformatics","biopython","comparative-genomics","genbank","genomics","genomics-visualization","microbial-genomics","python","streamlit","visualization","webapp"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/moshi4.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null}},"created_at":"2021-11-12T08:08:11.000Z","updated_at":"2024-12-26T23:40:38.000Z","dependencies_parsed_at":"2022-08-28T04:23:52.786Z","dependency_job_id":null,"html_url":"https://github.com/moshi4/GBKviz","commit_stats":null,"previous_names":[],"tags_count":12,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moshi4%2FGBKviz","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moshi4%2FGBKviz/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moshi4%2FGBKviz/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moshi4%2FGBKviz/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/moshi4","download_url":"https://codeload.github.com/moshi4/GBKviz/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":234882553,"owners_count":18901291,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","biopython","comparative-genomics","genbank","genomics","genomics-visualization","microbial-genomics","python","streamlit","visualization","webapp"],"created_at":"2024-09-27T13:41:16.372Z","updated_at":"2025-10-01T16:30:31.711Z","avatar_url":"https://github.com/moshi4.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GBKviz: Genbank Data Visualization WebApp\n\n[![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)\n![Python3](https://img.shields.io/badge/Language-Python3-steelblue)\n![License](https://img.shields.io/badge/License-MIT-steelblue)\n[![Latest PyPI version](https://img.shields.io/pypi/v/gbkviz.svg)](https://pypi.python.org/pypi/gbkviz)\n[![Bioconda](https://img.shields.io/conda/vn/bioconda/gbkviz.svg?color=green)](https://anaconda.org/bioconda/gbkviz)\n[![CI](https://github.com/moshi4/GBKviz/actions/workflows/ci.yml/badge.svg)](https://github.com/moshi4/GBKviz/actions/workflows/ci.yml)\n\n## Overview\n\nGBKviz is a web-based Genbank data visualization and comparison tool developed with streamlit web framework.\nGBKviz allows user to easily and flexibly draw CDSs in user-specified genomic region (PNG or SVG format is available).\nIt also supports drawing genome comparison results by MUMmer.\nGenomeDiagram, a part of BioPython module, is used to draw the diagram.\nThis software is developed under the strong inspiration of [EasyFig](https://mjsull.github.io/Easyfig/).\n\n![GBKviz Demo GIF](https://raw.githubusercontent.com/moshi4/GBKviz/main/src/gbkviz/gbkviz_demo.gif)  \nIf you are interested, click [here](https://share.streamlit.io/moshi4/gbkviz/main/src/gbkviz/gbkviz_webapp.py) to try GBKviz on Streamlit Cloud.  \n\u003e:warning: Due to the limited resources in Streamlit Cloud, it may be unstable.\n\u003e When performing comparative analysis of users' genomic data, use the stable, locally installed version.\n\n## Installation\n\nGBKviz is implemented in Python3. MUMmer is required for genome comparison.\n\n**Install bioconda package:**\n\n    conda install -c bioconda -c conda-forge gbkviz\n\n**Install PyPI package:**\n\n    pip install gbkviz\n\n**Use Docker ([Docker Image](https://hub.docker.com/r/moshi4/gbkviz/tags)):**\n\n    docker pull moshi4/gbkviz:latest\n    docker run -d -p 8501:8501 moshi4/gbkviz:latest\n\n## Dependencies\n\n- [Streamlit](https://streamlit.io/)  \n  Simple web framework for data analysis\n\n- [BioPython](https://github.com/biopython/biopython)  \n  Utility tools for computational molecular biology\n\n- [MUMmer](https://github.com/mummer4/mummer)  \n  Genome alignment tool for comparative genomics\n  \n## Command Usage\n\nLaunch GBKviz in web browser (\u003chttp://localhost:8501\u003e):\n\n    gbkviz_webapp\n  \nIf you are using Docker to start, above command is already executed.\n\n## Example\n\nExample of GBKviz genome comparison and visualization results.  \n\n![GBKviz Example Fig1](https://raw.githubusercontent.com/moshi4/GBKviz/main/image/gbkviz_example1.png)  \nFig.1: 4 phage whole genomes comparison result\n\n![GBKviz Example Fig2](https://raw.githubusercontent.com/moshi4/GBKviz/main/image/gbkviz_example2.png)  \nFig.2: 4 E.coli partial genomes comparison result\n\n![GBKviz Example Fig3](https://raw.githubusercontent.com/moshi4/GBKviz/main/image/gbkviz_example3.png)  \nFig.3: 4 E.coli whole genomes comparison result\n\n![GBKviz Example Fig4](https://raw.githubusercontent.com/moshi4/GBKviz/main/image/gbkviz_example4.png)  \nFig.4: Simple CDS visualization with gene label\n\n## Genome Comparison\n\nIn GBKviz, [MUMmer](https://github.com/mummer4/mummer) is used as genome comparison tool.\nFollowing four genome comparison methods are available.\n\n- Nucleotide One-to-One Mapping\n- Nucleotide Many-to-Many Mapping\n- Protein One-to-One Mapping\n- Protein Many-to-Many Mapping\n\nUser can download and check genome comparison results file.  \nGenome comparison results file is in the following tsv format.  \n\n| Columns      | Contents                                            |\n| ------------ | --------------------------------------------------- |\n| REF_START    | Reference genome alignment start position           |\n| REF_END      | Reference genome alignment end position             |\n| QUERY_START  | Query genome alignment start position               |\n| QUERY_END    | Query genome alignment end position                 |\n| REF_LENGTH   | Reference genome alignment length                   |\n| QUERY_LENGTH | Query genome alignment length                       |\n| IDENTITY     | Reference and query genome alignment identity (%)   |\n| REF_NAME     | Reference genome name tag                           |\n| QUERY_NAME   | Query genome name tag                               |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoshi4%2Fgbkviz","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmoshi4%2Fgbkviz","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoshi4%2Fgbkviz/lists"}