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Author: Xiaoting Hua

Email: [email protected]

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.

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 execute python 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 bacant create a virtual environment.Then conda install -c bacant -c conda-forge -c bioconda bacant install bacant.

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:

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