😸 MCAAT - Metagenomic CRISPR Array Analysis Tool

• CRISPR-Cas is a bacterial immune system also famous for its use in genome editing. The diversity of known systems could be significantly increased by metagenomic data.
• Here we present the Metagenomic CRISPR Array Analysis Tool MCAAT, a highly sensitive algorithm for finding CRISPR Arrays in un-assembled metagenomic data.
• It takes advantage of the properties of CRISPR arrays that form multicycles in de Bruijn graphs.

- MCAAT's assembly-free graph-based strategy outperforms assembly-based workflows and other assembly-free methods on synthetic and real metagenomes.

🥳 NEWS

Docker container available under: https://hub.docker.com/r/feeka94/mcaat

Installation using docker

Docker Build

bash docker build -t mcaat .

Run the Tool Using Docker

Mount your working directory to access input/output files:

bash docker run --rm -v $(pwd):/data mcaat \ --input_files /data/reads_R1.fastq /data/reads_R2.fastq \ --output-folder /data/results

Final Image Size

The final image is based on debian:bookworm-slim and includes only:

• The mcaat binary
• Runtime libraries: libomp5, zlib1g

This keeps the image small and portable.

Clean Up

To remove the image:

bash docker rmi mcaat

Compiling the project

🔧 Build the Project

To allow ./install.sh make changes, we execute following command: bash chmod +x ./install.sh You can build the project and the working version will be saved in the build folder. bash ./install.sh It is also possible to install the library by simply putting the --install flag. bash ./install.sh --install To clean up you can use --clean flag.

Usage

bash ./mcaat --input-files <file1> [file2] [--ram <amount>] [--threads <num>] [--output-folder <path>] [--help]

🧾 Command-Line Arguments

✅ Required

| Argument | Description | |---------------------------|-----------------------------------------------------------------------------| | --input_files <file1> [file2] | One or two input FASTA/FASTQ files. If one file is provided, it is treated as single-end data. If two files are provided, they are treated as paired-end reads. |

⚙️ Optional

| Argument | Description | |---------------------------|-----------------------------------------------------------------------------| | --ram <amount> | Maximum RAM to use. Units: B, K, M, G.
Default: 95% of system RAM
Example: --ram 4G | | --threads <num> | Number of threads to use.
Default: total CPU cores minus 2 | | --output-folder <path> | Output directory for results.
If not provided, a timestamped folder will be created automatically. If provided, the folder is used exactly as given. | | --help, -h | Show usage information and exit |

📁 Output Structure

The tool creates the following directory structure inside the specified output folder:

<output-folder>/ ├── CRISPR_Arrays.txt # Raw CRISPR array output

🧪 Example Usage

| Scenario | Command | |-----------------------------|-------------------------------------------------------------------------| | Paired-end input with custom output | ./mcaat --input_files reads_R1.fastq reads_R2.fastq --ram 8G --threads 12 --output-folder results/my_run | | Single-end input with default output | ./mcaat --input_files reads.fastq
Creates a folder like mcaat_run_2025-07-07_15-30-00/ |

Notes

• Input files must exist and be accessible.
• If RAM is set below 1 GB or above system capacity, the program will exit with an error.
• If only one input file is provided, the tool assumes single-end data.

Requirements

• C++17 compiler
• RapidFuzz (for fuzzy string matching)
• Filesystem support (<filesystem>)

Support

If you encounter issues or have questions, feel free to open an issue.