BBSniffer

BBSniffer is a software designed to identify suitable chassis strains from a comprehensive strain library, which encompasses pathogens, industrial microorganisms, and various non-pathogenic species, using specified biopolymer terms. It accomplishes this by analyzing biopolymer rules, HMM profiles, and genomic sequences derived from the user's input.

1 Data Download and Extraction

Use the following DOI links to download the data files from Zenodo (https://zenodo.org/), and untar the downloaded data files to a directory

• 10.5281/zenodo.8286952
• 10.5281/zenodo.8313016
• 10.5281/zenodo.8318303
• 10.5281/zenodo.8321312
• 10.5281/zenodo.8321340
• 10.5281/zenodo.8325104

2 Running the pipeline

2.1 Creating Input file

Edit input file according to your project. Input file format was provided as below:

{
    "Query": "(pf16570 OR pf16569 OR pf16555) and (ipr042002)",
    "Input_genomes": "Input_genomes",
    "Email": "somebody@123.com",
    "Antismash_threads": 10,
    "Antismash_gap_len": 20,
    "Antismash_extenson_len": 8
}

1. Query
   Input Protein family ID. Same category of protein families should be included in one parenthesis and linked by ' OR ', Different categories of protein families shold be linked with ' and '.
2. Input_genomes
   Name of folder which contains input reference model strain's complete genome file(s).
3. Email
   Email of users.
4. Antismash_threads
   Thread number when runnning antismash. Higher thread number may reduce run time but may cost more computing resources.
5. Antismash_gap_len
   Maximum length(in kbp) of gap region between elements in one BGC.
6. Antismash_extenson_len
   Length(in kbp) of flanking region of BGC's core region.

2.2 Clone git repository

Clone git repository of BBSniffer.

git clone https://github.com/xbiome/BBSniffer.git
cd BBSniffer

2.3 Build your Docker image

Build Docker image in users' PC or HPC cluster. Command is shown blow, content quoted by single quote after '-t' is the name and version info of Docker image, separated by ":".

docker build -t 'bbsniffer:1' .

2.4 Run program in command line

Run the pipeline with following command:

docker run -i --rm -v WORK_DIR:/in  bbsniffer:1 bash -c "python /opt/DockerImage/main.py -json /in/test.json -workdir /in/ --database /path/to/your/database/"

Users should substitute 'WORK_DIR' with their own working directory, replace 'bbsniffer:1' with their defined info from previous step and change the parameters in test.json file. Other command should be remained the same.

2.5 Run Protein Keywords searching

This scritp could be used to search Keywords in protein database (PFAM) and acquire relevant protein family ID.

docker run -i --rm -v WORK_DIR:/in  bbsniffer:1 bash -c "python /opt/DockerImage/KeywordsSearch.py -work_dir /in/ -input_keywords 'gram positive pilin'"

Check ProteinID.list file in working directory after the finish of the pipeline.

3. Tutorial for Windows users

3.1 Installation of WSL2

For Windows Users, the installation of WSL(Windows Subsystem for Linux) is required.
Follow this link for complete installation of WSL(Windows Subsystem for Linux) on Windows 10 system PC.
👍 Note: Ubuntu is recommanded in Step6 👍

3.2 Installation of latest Docker Desktop

Follow this link for complete installation of Docker Desktop.

3.3 Running BBSniffer on WSL

Open Ubuntu from your software list, login and Run pipeline following the instruction in Session 1

4. System requirement

4.1 Linux

• Avaiable space of system hard drive should be no less than 200G.

4.2 Windows

• 1903 or higher version are required for x64 system.
• 2004 or higher version are required for ARM system.
• WSL 2 is not supported on system lower than 18362.
• Avaiable space of system hard drive should be no less than 200G.

5. Citation

Huang, Y., Wu, Y., Hu, H. et al. Accelerating the design of pili-enabled living materials using an integrative technological workflow. Nat Chem Biol (2023). https://doi.org/10.1038/s41589-023-01489-x