Lineage Detector
Fast detection of emerging SARS-CoV-2 lineages via UShER phylogenetic placement, described in a sole-author preprint on bioRxiv (2024).
Lineage Detector is a bioinformatics tool for rapidly identifying newly emerging SARS-CoV-2 lineages from genomic sequence data. Built on the UShER phylogenetic placement framework, it efficiently assigns Pango lineage designations to novel viral sequences.
As a volunteer Pango lineage spotter since 2023, I have contributed to global SARS-CoV-2 surveillance by proposing and curating new lineage designations. This tool automates key parts of that workflow.
Code and documentation are on GitHub; see also the bioRxiv preprint and the designated Pango lineages I proposed.