https://github.com/xthua/bacant
This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
https://github.com/xthua/bacant
amr bacteria fasta integron transposon
Last synced: 5 months ago
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This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
- Host: GitHub
- URL: https://github.com/xthua/bacant
- Owner: xthua
- License: gpl-3.0
- Created: 2020-10-21T07:55:00.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2023-05-16T01:09:08.000Z (about 3 years ago)
- Last Synced: 2026-01-02T19:20:24.007Z (5 months ago)
- Topics: amr, bacteria, fasta, integron, transposon
- Language: F*
- Homepage:
- Size: 49.8 MB
- Stars: 21
- Watchers: 1
- Forks: 7
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
Author: Xiaoting Hua
Email: xiaotinghua@zju.edu.cn
institute: Key laboratory of Microbiol technology and Bioinformatics of Zhejiang Province
This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
### Install:
Bacant is a python3.X script, running on linux.
You 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.
* First:
You can download from github by `git clone https://github.com/xthua/bacant.git`. Then execute `python setup.py install`.
* Second:
You can install BacAnt from [PyPI](https://pypi.org/project/BacAnt) by `pip install BacAnt`.
* Third:
You can install BacAnt from [anaconda](https://anaconda.org/bacant/bacant).
First,`conda create -n bacant` create a virtual environment.Then `conda install -c bacant -c conda-forge -c bioconda bacant ` install bacant.
### Run:
BacAnt can accept FASTA and GENBANK format file(single or multi sequences in one file). Attention on GENBANK format file, it should follow standard format.
There are three input parameter, "-n" means FASTA, "-g" means GENBANK, "-D" means input dir contains FASTA or GENBANK.
* Simply, you can just run:
```
bacant -n FASTA -o outdir
bacant -g GENBANK -o outdir
bacant -D input_dir -o outdir
```
* For more parameter, you can run:
```
bacant -h
```
* Here are some import parameter:
parameter | description
---- | -----
--nucleotide(-n) | FASTA file
--genbank(-g) | GENBANK file
--indir(-D) | input dirname
--resultdir(-o) | output dirname
--databases(-d) | reference databases,default is ResDB,IntegronDB,TransposonDB
--coverages(-c) | filtering coverage, default is "60,60,60", three numbers represents AMR,In,Tn in turn
--identities(-i) | filtering identity, default is "90,90,90", three numbers represents AMR,In,Tn in turn
### Databases:
We 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).
User can define their custom databases, and when run bacant ,just add parameter -p(--path) for databases dirname.
Here are databases structure:
.
├── IntegronDB
│ ├── Integron.fasta Integron reference sequences in FASTA format
│ │ sequence id must be description|accession,eg: In0|PAU49101
│ ├── Integron.nhr
│ ├── Integron.nin
│ └── Integron.nsq
├── ResDB
│ ├── Res.fasta Resistance gene reference sequences in FASTA format
│ │ sequence id must be database name~~~gene~~~accession~~~description,
│ │ eg: ncbi~~~1567214_ble~~~NG_047553.1~~~BLEOMYCIN BLMA family bleomycin binding protein
│ ├── Res.nhr
│ ├── Res.nin
│ └── Res.nsq
└── TransposonDB
├── Transposon.fasta Transposon reference sequences in FASTA format
│ sequence id must be description|accession,eg: Tn2009|CP001937
├── Transposon.nhr
├── Transposon.nin
└── Transposon.nsq
### Output:
filename | description
---- | -----
*.gb | GENBANK format annotation
AMR.tsv | filtered resistance annotation
AMR.possible.tsv | all possible resistance annotation
replicon.tsv | replicon annotation
integron.filter.tsv | most like integron
integron.detail.tsv | integron_finder result,detail descripton of integron structure
transposon.filter.tsv | transposon element after overlap screen
transposon.possible.tsv | all possible transposon element
annotation.html | output visualization