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AutoLin is a powerful tool designed to enhance Nextstrain Auspice JSON files by adding lineage nomenclature labels using the genotype representation index heuristic. Explore the intricate lineage relationships within your genomic data with AutoLin today.

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Use Cases Limitations Evidence Owner's Insight

This app generates genotype-based and hierarchical nomenclature, akin to a simplified Pango-style naming schema. AutoLin iteratively generates labels, ensuring mutually exclusive lineage assignments based on user-defined conditions and proportions of samples. It seamlessly integrates with Auspice v2 format JSON files, ideally those containing mutation annotations and amino acid change translations. Users can easily upload the enhanced JSON files to Auspice for visualization.

See owner's GitHub repository for more information: https://github.com/jmcbroome/automated-lineage-json.

This work is based on the paper:

McBroome, J., Schneider, A. d. B., Roemer, C., Wolfinger, M. T., Hinrichs, A. S., O’Toole, A. N., Ruis, C., Turakhia, Y., Rambaut, A., & Corbett-Detig, R. (2023). Automated Agnostic Designation of Pathogen Lineages. bioRxiv, 2023.02.03.527052. https://doi.org/10.1101/2023.02.03.527052

This application was not uploaded by the author, but through their publicly available Github repository, https://github.com/jmcbroome/automated-lineage-json.

Prototype

Warning: Not intended for clinical use. Assume outputs are unsafe and unvalidated. Use carefully.


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