Resources

Source code & citations

Every ARGUS platform is open source, MIT-licensed, and reproducible from its generator scripts. If you use a platform in your research, please cite the pipeline and the underlying dataset.

Source code

All generator scripts, CSS, and embedded data pipelines are available under the MIT license.

Core citations

Each platform carries its own citation block on its landing page. Cite the specific pipeline and the underlying dataset used for that platform.

🦖 SAURUS Pipeline
Beckley B, Amarh V. StaphScope: a species-optimized computational pipeline for rapid and accessible Staphylococcus aureus genotyping and surveillance. BMC Genomics. 2026;27:261.
doi:10.1186/s12864-026-12609-x
🦖 SAURUS Gene data
Shelenkov A, Slavokhotova A, Yunusova M, et al. Genomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Staphylococcus aureus. BMC Genom Data. 2025;26:65.
doi:10.1186/s12863-025-01363-w
🌑 ECLIPSE Pipeline
Beckley B, Amarh V. EcoliTyper: a species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. BMC Bioinformatics. 2026;27(1):182.
doi:10.1186/s12859-026-06529-6
🌊 ABYSS Pipeline
Beckley B, Amarh V, Lopes BS, et al. AcinetoScope: a computational pipeline for rapid, comprehensive Acinetobacter baumannii outbreak investigation and resistance gene tracking. Scientific Reports. 2026.
doi:10.1038/s41598-026-70189-y
🌊 ABYSS Gene data
Shelenkov A, Mikhaylova Y, Akimkin V. Genomic Epidemiology Dataset for the Important Nosocomial Pathogenic Bacterium Acinetobacter baumannii. Data. 2024;9(2):22.
doi:10.3390/data9020022

Metadata source

Country of origin, isolation source, host species, and collection year are extracted from NCBI BioSample records via the NCBI Datasets command-line tool. Field names (geo_loc_name, isolation_source, host, collection_date) are parsed from the standard BioSample attribute list and stored alongside the accession in a metadata table.

Genome accessions and assembly metadata are retrieved from NCBI Assembly under taxonomy IDs appropriate for each species.