bacant

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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.

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 by pip install BacAnt.
• Third: 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.

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:

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: