AI-Assisted Genome Assembly for Pathogen Surveillance

Spades is a bioinformatics tool used by the NYC Department of Health and Mental Hygiene's Public Health Laboratory to reconstruct the genetic sequences of bacteria and other pathogens from raw laboratory sequencing data. It assembles draft genomes that scientists use to identify organism types, detect antibiotic resistance, and track disease outbreaks. The tool operates on biological sample data with no personal identifying information. It runs as an intermediate computational step in laboratory workflows and does not make decisions about individuals.