# CheckAMG
**Automated curation of Auxiliary Metabolic Genes (AMGs), Auxiliary Regulatory Genes (AReGs), and Auxiliary Physiology Genes (APGs) in viral genomes.**
> ⚠️ **This tool is in active development and has not yet been peer-reviewed.**
## Quick Usage
```bash
checkamg download -d /path/to/db/destination
checkamg annotate \
-d /path/to/db/destination \
-g examples/example_data/single_contig_viruses.fasta \
-vg examples/example_data/multi_contig_vMAGs \
-o CheckAMG_example_out
```
## Features
* Input: nucleotide or protein sequences
* Handles single-contig viral genomes and multi-contig vMAGs
* Functional annotation + viral genome context-based curation
* Outputs curated lists and amino-acid sequences of AMGs, AReGs, and APGs
## Command-line Modules
```bash
checkamg -h
```
* `download`: Get required databases
* `annotate`: Predict and curate AVGs
* `de-novo`, `aggregate`, `end-to-end`: Coming soon
## Example Output
* FASTA files of predicted AVGs (by confidence and function class)
* Tabular summary of predictions (`final_results.tsv`, `gene_annotations.tsv`)
## License
GPL-3.0-or-later
**Example data and full documentation:**
[https://github.com/AnantharamanLab/CheckAMG](https://github.com/AnantharamanLab/CheckAMG)
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"description": "# CheckAMG\n\n**Automated curation of Auxiliary Metabolic Genes (AMGs), Auxiliary Regulatory Genes (AReGs), and Auxiliary Physiology Genes (APGs) in viral genomes.**\n\n> \u26a0\ufe0f **This tool is in active development and has not yet been peer-reviewed.**\n\n## Quick Usage\n\n```bash\ncheckamg download -d /path/to/db/destination\n\ncheckamg annotate \\\n -d /path/to/db/destination \\\n -g examples/example_data/single_contig_viruses.fasta \\\n -vg examples/example_data/multi_contig_vMAGs \\\n -o CheckAMG_example_out\n```\n\n## Features\n\n* Input: nucleotide or protein sequences\n* Handles single-contig viral genomes and multi-contig vMAGs\n* Functional annotation + viral genome context-based curation\n* Outputs curated lists and amino-acid sequences of AMGs, AReGs, and APGs\n\n## Command-line Modules\n\n```bash\ncheckamg -h\n```\n\n* `download`: Get required databases\n* `annotate`: Predict and curate AVGs\n* `de-novo`, `aggregate`, `end-to-end`: Coming soon\n\n## Example Output\n\n* FASTA files of predicted AVGs (by confidence and function class)\n* Tabular summary of predictions (`final_results.tsv`, `gene_annotations.tsv`)\n\n## License\n\nGPL-3.0-or-later\n\n**Example data and full documentation:**\n[https://github.com/AnantharamanLab/CheckAMG](https://github.com/AnantharamanLab/CheckAMG)\n",
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