HiFiBGC

HiFiBGC is a tool for detecting Biosynthetic Gene Clusters (BGCs) in PacBio HiFi metagenomic data.

Table of Contents

• Installation
• Usage
• Output
• Commands
• Third-party Tools
• Citation

Installation

Choose one of the following installation methods:

Option 1: mamba (recommended)

mamba create -n hifibgc -c conda-forge -c bioconda -c amityadav -y hifibgc
mamba activate hifibgc

mamba is preferred over below conda as it takes much lesser time and consumes lesser memory (RAM).
mamba can be installed from here.

Option 2: conda

conda create -n hifibgc -c conda-forge -c bioconda -c amityadav -y hifibgc
conda activate hifibgc

Option 3: pip

Requires Python 3.11, pip, and mamba:

pip install hifibgc

Note: HiFiBGC can run without mamba, but then every command need to be run with --conda-frontend conda (e.g., hifibgc test --conda-frontend conda).

Test installation

Install prerequisites

Run once to install the required database and tool:

hifibgc install

Run on a test dataset

Verify the installation using the test dataset:

hifibgc test

Successful completion will display "Snakemake finished successfully" and create an output directory hifibgc1.out.

OS Compatibility: Installation has been tested on Ubuntu 20.04 (Linux) and macOS-12. On macOS-12, installation was verified using conda and pip, but not mamba.

Usage

Install prerequisites

Run once to install the required database and tool (note: if you have already run this earlier for testing installation, then skip this step):

hifibgc install

Run on your own data

To run HiFiBGC on your own data, use the following command:

hifibgc run --input input.fastq

By default, HiFiBGC outputs to a directory named hifibgc1.out, you can specify a custom name using --output option as shown below. The count of threads can be specified via --threads option (the default is 80).

hifibgc run --input input.fastq --output outdir --threads 50

For all available options, see Run command help.

Output

The output directory structure:

hifibgc1.out/
├── 01_assembly/                 # Output from three assemblers
├── 02_mapping_reads_to_merged_assembly/  # Read mapping to concatenated assembly and unmapped read extraction
├── 03_antismash/                # BGC prediction
├── 04_bgc_clustering/           # BGC clustering
├── 05_final_output/             # Primary HiFiBGC output
├── benchmarks/                  # Resource usage and timing information for different components of HiFiBGC
├── config.yaml                  # Configuration file for HiFiBGC run
├── hifibgc.log                  # Snakemake log file
└── logs/                        # Tool-specific log files

Among above, the folder 05_final_output contains primary output of HiFiBGC with below directory structure.

05_final_output/                 # Primary HiFiBGC output
├── BGC_all/                     # All BGC .gbk files
├── BGC_all_metadata.tsv         # Metadata for all BGCs
├── BGC_representative/          # Representative BGC .gbk files
└── upsetplot/                   # Upsetplot comparison of results from three assemblers and unmapped reads

Commands

Main help

$ hifibgc --help

Usage: hifibgc [OPTIONS] COMMAND [ARGS]...

  Detect Biosynthetic Gene Clusters (BGCs) in HiFi metagenomic data. For
  more options, run: hifibgc command --help

Options:
  -v, --version  Show the version and exit.
  -h, --help     Show this message and exit.

Commands:
  run       Run HiFiBGC
  install   Install required database and tool
  test      Test HiFiBGC
  config    Copy the system default config file
  citation  Print the citation(s) for this tool

Run command help

$ hifibgc run --help

Usage: hifibgc run [OPTIONS] [SNAKE_ARGS]...

  Run HiFiBGC

Options:
  --input TEXT                  Input file  [required]
  --output PATH                 Output directory  [default: hifibgc1.out]
  --bigscape_cutoff FLOAT       BiG-SCAPE cutoff parameter  [default: 0.3]
  --configfile TEXT             Custom config file [default:
                                (outputDir)/config.yaml]
  --threads INTEGER             Number of threads to use  [default: 80]
  --use-conda / --no-use-conda  Use conda for Snakemake rules  [default: use-
                                conda]
  --conda-prefix PATH           Custom conda env directory
  --snake-default TEXT          Customise Snakemake runtime args  [default:
                                --rerun-incomplete, --printshellcmds,
                                --nolock, --show-failed-logs]
  -h, --help                    Show this message and exit.

For detailed usage of other commands, use hifibgc <command> --help.

Third-party tools

HiFiBGC utilizes following tools:

• hifiasm-meta
• metaFlye
• HiCanu
• Minimap2
• SAMtools
• antiSMASH
• BiG-SCAPE
• complex-upsetplot
• Snaketool
• Snaketool-utils

Citation

Yadav, A., Subramanian, S. HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes. BMC Genomics 25, 1096 (2024). https://doi.org/10.1186/s12864-024-10950-7