fIDBAC

fIDBAC integrated an accuracy bacterial identification, automated strain typing and downstream AR/VF gene prediction analysis in a single, coherent workflow, the website is http://fbac.dmicrobe.cn/

Installtion

First download part of the database and code, and then install the dependent software mentioned in the requirements.txt file.

git clone https://github.com/DMicrobe/fIDBAC.git

Requirements

• perl
• Python3
  The packages that need to be installed are "Biopython scipy skbio gzip Levenshtein".
• NCBI BLAST+ 2.10.1
• kmerfinder 1.0.9
• FastANI here
• Prokka 1.14.6
• Prodigal V2.6.3
• RGI here
• Phylip here
• MUMmer 3.23
• ANIcalculator v1.0

You can also install this softwares with using conda. Due to dependency conflicts, we recommend installing RGI in a different environment from other software. After this software are installed, write the path to the file config_db.txt.

Download data

• Download Type strains genome and gene files in 12784.genome.txt . Construct a configuration file, format reference file, write ACC ID, genome and gene path into the file type.
• Download kmerdb and close snp data here .
• Download PubMLST database here .

Test

perl script/fIDBAC.pl  -input example/example.fa -outdir ./ -temp ./