AI-Assisted DNA Basecalling for Genomic Surveillance

Guppy is a neural network tool used by the NYC Department of Health and Mental Hygiene's Public Health Laboratory to convert raw electrical signals from DNA sequencing instruments into readable genetic sequences. It is used a few times per month on clinical and surveillance specimens — including for COVID-19 genomic analysis — and does not collect or disclose any identifying information about individuals. The resulting sequence data is used for downstream outbreak analysis and public health surveillance.