Viral genomes, PCR assays and primers, measured on real sequence data. 3 projects, each with its code on GitHub.
Do published PCR diagnostic assays still match what is circulating? 2,765 GenBank genomes, five published assays, zero dependencies.
Genomic surveillance for Cotton Leaf Curl Virus on real NCBI GenBank sequences: which variant is rising and is that real, is anything selecting for it, and how are strains related. Collapsing clonal duplicates turned 9 'emerging variants' into 0.
Diagnostic PCR primers that survive viral drift. Nearest-neighbour thermodynamics, conservation analysis, degenerate primers, and alerts when a deployed assay starts going blind because a mutation landed at the 3-prime end.