{"id":37077909,"url":"https://github.com/xthua/bacant","last_synced_at":"2026-01-14T09:02:27.910Z","repository":{"id":57413619,"uuid":"305949386","full_name":"xthua/bacant","owner":"xthua","description":"This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.","archived":false,"fork":false,"pushed_at":"2023-05-16T01:09:08.000Z","size":52184,"stargazers_count":21,"open_issues_count":4,"forks_count":7,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-01-02T19:20:24.007Z","etag":null,"topics":["amr","bacteria","fasta","integron","transposon"],"latest_commit_sha":null,"homepage":"","language":"F*","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/xthua.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2020-10-21T07:55:00.000Z","updated_at":"2025-05-22T01:56:44.000Z","dependencies_parsed_at":"2022-09-15T03:41:14.104Z","dependency_job_id":"b5b08478-cf59-4865-84ae-f5aab6ea5c7d","html_url":"https://github.com/xthua/bacant","commit_stats":{"total_commits":117,"total_committers":1,"mean_commits":117.0,"dds":0.0,"last_synced_commit":"eff1b62d285557a6e14f260b89bb39aeffc74da9"},"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/xthua/bacant","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xthua%2Fbacant","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xthua%2Fbacant/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xthua%2Fbacant/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xthua%2Fbacant/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xthua","download_url":"https://codeload.github.com/xthua/bacant/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xthua%2Fbacant/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28338971,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-12T10:58:46.209Z","status":"ssl_error","status_checked_at":"2026-01-12T10:58:42.742Z","response_time":98,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["amr","bacteria","fasta","integron","transposon"],"created_at":"2026-01-14T09:02:27.280Z","updated_at":"2026-01-14T09:02:27.904Z","avatar_url":"https://github.com/xthua.png","language":"F*","funding_links":[],"categories":[],"sub_categories":[],"readme":"Author:     Xiaoting Hua\n\nEmail:      xiaotinghua@zju.edu.cn\n\ninstitute:  Key laboratory of Microbiol technology and Bioinformatics of Zhejiang Province\n\nThis program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.\n\n### Install:\nBacant is a python3.X script, running on linux. \nYou should install BLAST and add it in environment variable, you can download from `https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/`. BLAST version is 2.7.1 in bacant.\n\n* First:\n  You can download from github by `git clone https://github.com/xthua/bacant.git`. Then execute `python setup.py install`.\n* Second:\n  You can install BacAnt from [PyPI](https://pypi.org/project/BacAnt) by `pip install BacAnt`.\n* Third:\n  You can install BacAnt from [anaconda](https://anaconda.org/bacant/bacant).\n  First,`conda create -n bacant` create a virtual environment.Then `conda install -c bacant -c conda-forge -c bioconda bacant ` install bacant.\n\n### Run:\nBacAnt can accept FASTA and GENBANK format file(single or multi sequences in one file). Attention on GENBANK format file, it should follow standard format.\nThere are three input parameter, \"-n\" means FASTA, \"-g\" means GENBANK, \"-D\" means input dir contains FASTA or GENBANK.\n* Simply, you can just run:\n```\nbacant -n FASTA -o outdir\nbacant -g GENBANK -o outdir\nbacant -D input_dir -o outdir\n```\n* For more parameter, you can run:\n```\nbacant -h\n```\n* Here are some import parameter:\n\nparameter  | description\n---- | -----\n--nucleotide(-n) | FASTA file\n--genbank(-g) | GENBANK file\n--indir(-D) | input dirname\n--resultdir(-o) | output dirname\n--databases(-d) | reference databases,default is ResDB,IntegronDB,TransposonDB\n--coverages(-c) | filtering coverage, default is \"60,60,60\", three numbers represents AMR,In,Tn in turn\n--identities(-i) | filtering identity, default is \"90,90,90\", three numbers represents AMR,In,Tn in turn\n\n### Databases:\nWe have updated database to v2.0(2021.05.11) since BacAnt-v3.3.1. You can download from [here](http://bacant.net/static/database/v2.0/bacant-db-v2.0.tar.gz).\nUser can define their custom databases, and when run bacant ,just add parameter -p(--path) for databases dirname.\nHere are databases structure:\n\n\u003cpre\u003e\n  .\n  ├── IntegronDB\n  │   ├── Integron.fasta    Integron reference sequences in FASTA format\n  │   │                     sequence id must be description|accession,eg: In0|PAU49101\n  │   ├── Integron.nhr\n  │   ├── Integron.nin\n  │   └── Integron.nsq\n  ├── ResDB\n  │   ├── Res.fasta         Resistance gene reference sequences in FASTA format\n  │   │                     sequence id must be database name~~~gene~~~accession~~~description,\n  │   │                     eg:  ncbi~~~1567214_ble~~~NG_047553.1~~~BLEOMYCIN BLMA family bleomycin binding protein\n  │   ├── Res.nhr\n  │   ├── Res.nin\n  │   └── Res.nsq\n  └── TransposonDB\n      ├── Transposon.fasta  Transposon reference sequences in FASTA format\n      │                     sequence id must be description|accession,eg: Tn2009|CP001937\n      ├── Transposon.nhr\n      ├── Transposon.nin\n      └── Transposon.nsq\n\u003c/pre\u003e      \n### Output:\n\nfilename  | description\n---- | -----\n*.gb | GENBANK format annotation\nAMR.tsv | filtered resistance annotation\nAMR.possible.tsv | all possible resistance annotation\nreplicon.tsv | replicon annotation\nintegron.filter.tsv | most like integron\nintegron.detail.tsv | integron_finder result,detail descripton of integron structure\ntransposon.filter.tsv | transposon element after overlap screen\ntransposon.possible.tsv | all possible transposon element\nannotation.html | output visualization\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxthua%2Fbacant","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fxthua%2Fbacant","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxthua%2Fbacant/lists"}