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Fix formatting in README.md
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readme.md

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## 😸 MCAAT - Metagenomic CRISPR Array Analysis Tool
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## MCAAT - Metagenomic CRISPR Array Analysis Tool
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> [!IMPORTANT]
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> The tool is currently in heavy development. We are testing new functionalities like spacer ordering, CAS gene detection and protospacer detection. PLEASE USE DOCKER: [https://hub.docker.com/r/feeka94/mcaat](https://hub.docker.com/r/feeka94/mcaat)
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- MCAAT's assembly-free graph-based strategy outperforms assembly-based workflows and other assembly-free methods on synthetic and real metagenomes.
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### 🥳 NEWS
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### NEWS
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- Docker container available under: https://hub.docker.com/r/feeka94/mcaat
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- Version 0.3 makes use of following optimization techniques:
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- Better data structures for preprocessing, `phmap::flat_hash_set`
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### Compiling the project
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#### 🔧 Build the Project
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#### Build the Project
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To allow ./install.sh make changes, we execute following command:
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```bash
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chmod +x ./install.sh
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```
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### 🧾 Command-Line Arguments
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### Command-Line Arguments
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#### Required
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#### Required
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| Argument | Description |
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|---------------------------|-----------------------------------------------------------------------------|
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| `--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. |
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#### ⚙️ Optional
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#### Optional
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| Argument | Description |
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|---------------------------|-----------------------------------------------------------------------------|
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### 📁 Output Structure
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### Output Structure
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The tool creates the following directory structure inside the specified output folder:
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### 🧪 Example Usage
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### Example Usage
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| Scenario | Command |
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|-----------------------------|-------------------------------------------------------------------------|
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### ⚙️ Settings file support
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### Settings file support
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Create a simple key=value text file (one setting per line) and pass it with `--settings /path/to/file`.
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