checkamg 0.10.0

Automated discovery and curation of Auxiliary Metabolic Genes (AMGs), Auxiliary Regulatory Genes (AReGs), and Auxiliary Physiology Genes (APGs) encoded by viral genomes.

CheckAMG

Automated discovery and curation of Auxiliary Metabolic Genes (AMGs), Auxiliary Regulatory Genes (AReGs), and Auxiliary Physiology Genes (APGs) encoded by viral genomes

⚠️ This tool is in active development and has not yet been peer-reviewed.

Quick Usage

checkamg download -d /path/to/db/destination

checkamg annotate \
  -d /path/to/db/destination \
  -i examples/example_data/single_contig_viruses.fasta \
  -I 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/bins
• Functional annotation + viral genome context-based curation
• Outputs curated lists and amino-acid sequences of AMGs, AReGs, and APGs

Command-line Modules

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