checkamg 1.0

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This tool is in active development and has not yet been peer-reviewed.

CheckAMG identifies and curates high-confidence auxiliary viral genes (AVGs) using two complementary approaches: a reference-based path (curated functional annotations plus viral genome context) and a reference-independent path (the Protein Set Transformer genome language model).

Quick usage

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

checkamg end-to-end \
  -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
• Reference-based annotation and genome-context curation (annotate)
• Reference-independent prediction with a protein genome language model (de-novo)
• Combined reporting (aggregate) and one-command runs (end-to-end)
• Outputs curated lists and amino-acid sequences of AMGs, AReGs, and APGs

Modules

checkamg -h

• download: get the required databases
• annotate: reference-based AVG prediction and curation
• de-novo: reference-independent AVG prediction with PST
• aggregate: merge annotate and de-novo results
• end-to-end: run annotate, de-novo, and aggregate in tandem
• train: finetune a custom CheckAMG-PST model

License

GPL-3.0-or-later

Installation, example data, and full documentation: https://github.com/AnantharamanLab/CheckAMG and the CheckAMG Wiki.