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This tool is in active development and has not yet been peer-reviewed.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: an annotation-based path (curated functional annotations plus viral genome context) and a annotation-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 databasesannotate: reference-based AVG prediction and curationde-novo: reference-independent AVG prediction with PSTaggregate: mergeannotateandde-novoresultsend-to-end: run annotate, de-novo, and aggregate in tandemtrain: 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.
1 maintainer
Metadata
1 maintainer
Release files for checkamg 1.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| checkamg-1.1.2.tar.gz | 13.9 MB | Details |
Release files / checkamg-1.1.2.tar.gz
| Download URL | checkamg-1.1.2.tar.gz |
|---|---|
| Size | 13.9 MB |
| Tags | Source |
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