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.
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.
git clone https://github.com/xthua/bacant.git
. Then execute python setup.py install
.pip install BacAnt
.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.
bacant -n FASTA -o outdir
bacant -g GENBANK -o outdir
bacant -D input_dir -o outdir
bacant -h
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 |
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
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 |