BGCpri

BGCpri is an application designed to prioritize biosynthetic gene clusters (BGCs) of polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid NRPS/PKS identified through antiSMASH results. It employs a scoring system tailored to prioritize BGCs with the potential to encode chemically diverse secondary metabolites.

Getting Started

BGCpri requires the unzip dependency to be installed:

Installing unzip

unzip is necessary for BGCpri to extract antiSMASH compressed .zip files.

For Debian-based systems (e.g., Ubuntu or Linux Mint) or Windows via Ubuntu WSL:

sudo apt update && sudo apt install unzip

For Redhat distributions (e.g., Fedora or CentOS):

sudo dnf install unzip

For Arch-based distributions (e.g., Arch Linux and Manjaro):

sudo pacman -S unzip

For OpenSUSE:

sudo zypper install unzip

Installing BGCpri on Linux

To install BGCpri on a Linux system, follow these steps:

1. Download BGCpri

First, download the BGCpri application from the GitHub repository .

2. Extract BGCpri

Extract the downloaded BGCpri archive to a directory of your choice. You can do this by using the unzip command in the terminal.

unzip BGCpri.zip -d /path/to/extract

Replace /path/to/extract with the directory where you want to extract BGCpri.

3. Navigate to the BGCpri Directory

Open a terminal and navigate to the directory where you extracted BGCpri.

cd /path/to/extract/BGCpri

4. Set Permissions (if necessary)

Depending on your system's configuration, you may need to set executable permissions for the BGCpri executable file.

chmod +x BGCpri

5. Add BGCpri to PATH (highly recommended)

For convenience, you may want to add the directory containing the BGCpri executable to your system's PATH. This step is optional but can make it easier to run BGCpri from any directory in the terminal.

export PATH="/path/to/extract/BGCpri:$PATH"

Replace /path/to/extract/BGCpri with the actual path to the directory containing the BGCpri executable. You can add this line to your shell configuration file (e.g., ~/.bashrc, ~/.bash_profile, ~/.zshrc, etc.) to make the change permanent.

6. Verify Installation

To verify that BGCpri is installed correctly, open a new terminal window and type:

BGCpri --version

If installed properly, this command should display the version of BGCpri installed on your system.

Following these steps will enable you to successfully install BGCpri on your system.

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Using BGCpri

Once you have installed the dependencies and BGCpri itself, you can use it to prioritize Biosynthetic Gene Clusters based on antiSMASH results. Here's how you can get started:

1. Prepare antiSMASH Results

Ensure that you have run antiSMASH on your genome or metagenome of interest and obtained the result files in .zip or .gbk (for individual BGCs) format.

Also, check if the .gbk files contain the name of the strain in the ‘ORGANISM’ section, like the following example:

LOCUS       QZCE01000001           21245 bp    DNA     linear   BCT 25-FEB-2020
DEFINITION  Adonisia turfae CCMR0082 Scaffold_1a, whole genome shotgun sequence.
ACCESSION   QZCE01000001
VERSION     QZCE01000001.1
KEYWORDS    .
SOURCE      Adonisia turfae CCMR0082
  ORGANISM  Adonisia turfae CCMR0082

If it’s empty, run the following command to add the organism’s name on multiple .gbk files inside the same directory:

sed -i 's|  ORGANISM|  ORGANISM  StrainName|g' *.gbk

Replace ‘StrainName’ with the actual name of the strain.

2. Execute BGCpri

If you have installed BGCpri in your system, then run the following command:

BGCpri -i /path/to/antiSMASH/results -o /path/to/BGCpri/output/results

Replace ‘/path/to/antiSMASH/results’ with the actual path to the directory containing your antiSMASH results of interest and replace /path/to/BGCpri/output/results with the path to the desired output destination for the output results to be saved.

If you haven't installed BGCpri in your system, then navigate to the directory where the BGCpri executable is located and run the following command:

./BGCpri -i /path/to/antiSMASH/results -o /path/to/BGCpri/output/results

Replace ‘/path/to/antiSMASH/results’ with the actual path to the directory containing your antiSMASH results of interest and replace /path/to/BGCpri/output/results with the path to the desired output destination for the output results to be saved.

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BGCpri results

After the execution, BGCpri will create a directory called “BGC_PRIORITIZATION_RESULTS”. Inside this directory you will find the following archive:

BGC_summary.tsv: corresponds to the table of prioritization results.

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Contributing

Contributions to BGCpri are welcome! If you encounter any issues, have suggestions for improvements, or would like to contribute new features, please feel free to open an issue or submit a pull request on the GitHub repository.

License

BGCpri is licensed under the GPLLicense. See the LICENSE file for details.

Credits

BGCpri was developed by João Pedro Brandão Domingues, Lígia Akemi Mizuyama, Laura Pavan Ióca, Alessandra S. Eustáquio, and Camila Manoel Crnkovic.