Author: Hong Wenjie
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.
- One:
You can download from github by
git clone https://github.com/xthua/bacant.git. Then executepython setup.py install. - Two:
You can install BacAnt from PyPI by
pip install BacAnt. - Three:
You can install BacAnt from anaconda.
First,
conda create -n bacantcreate a virtual environment.Thenconda install -c bacant -c conda-forge -c bioconda bacantinstall 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. 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 |
