AI-Assisted Genomic Sequence Alignment for Disease Surveillance

Minimap2 is a bioinformatics tool used by the NYC Department of Health and Mental Hygiene's Public Health Laboratory to align DNA sequencing data to reference genomes for COVID-19 and monkeypox virus surveillance. It processes laboratory-generated sequencing reads — not personal information — to reconstruct complete genomic sequences used for public health characterization. No identifying information about individuals is collected or disclosed; the system operates on biological samples, not patient records. It runs approximately three to four times per week under laboratory staff supervision.