HTBGC-Finder

A tool for identifying potential horizontally transferred BGCs.

• Version：HTBGC-Finder V1.1.4
• Update：2024/07/31
• Project homepage: https://github.com/Shirly-Yang/HTBGC-Finder

Installation

conda (recommended)：

• conda create -n htbgcfinder python=3.7.0

• conda activate htbgcfinder

• conda install MicrobiomeX::htbgcfinder

• echo 'export PFAM_PATH="/your/path/to/miniconda3/envs/htbgcfinder/lib/python3.7/site-packages/antismash/databases/pfam/34.0"' >> ~/.bashrc

• The database of kraken2 is required but not supported by conda. If you have previously built the database, please skip this step and proceed to the next one.

• Skip this step if you have already built the database:

• kraken2-build --standard --threads 8 --db /your/path/to/kraken2database

• proceed with the following command to set the environment variable:

• echo 'export KRAKEN2_DB_PATH="/your/path/to/kraken2database/standard"'>> ~/.bashrc

• source ~/.bashrc

Tips： If you encounter the following error while building the database: rsync_from_ncbi.pl: unexpected FTP path (new server?), you can try the following solution: change if (! ($full_path =~ s#^ftp://ftp://${qm_server}${qm_server_path}/##)) in line 46 in the file /your/path/to/miniconda3/envs/htbgcfinder/libexec/rsync_from_ncbi.pl from ftp to https.

github：

• git clone https://github.com/Shirly-Yang/HTBGC-Finder
• dependencies
  • python=3.7.0
  • biopython=1.78
  • antismash=6.1.1
  • fastANI
  • bigscape
  • ncbi-genome-download
  • kraken2
  • An exemplary shell script dependencies.sh can be found in the root directory. This script file should be adjusted if you wish to place some files to different locations or use absolute path names.

Usage

conda：

• htbgcfinder -i /your/path/to/miniconda3/envs/htbgcfinder/bin/testdata/fna -o /your/path/to/miniconda3/envs/htbgcfinder/bin/testdata/result

github：

• python HTBGC-Finder.py -i ./testdata/fna -o ./testdata/result you can use python HTBGC-Finder.py -h to view available parameters.

Script

• HTBGCFinder.py: identify potential horizontally transferred BGCs
• fastani_run.py: Remove redundant MAGs
• kraken2_run.py: Perform species annotation
• antismash_run.py: Identify BGCs
• bigscape_run.py：Clustering BGC into gene cluster family (GCF)
• genome_download.py: Download corresponding reference genomes
• ref_BGC_fna.py: Identify BGCs
• phylotest.py: Perform phylogenetic analysis
• final_check.py: Identify potential horizontally transferred BGCs

If you If used this script, please cite the following article：