AI-Assisted Genome Assembly for Pathogen Surveillance
What it is for
- Spades is an intermediate computational step in public health laboratory workflows for bacterial analyses, supporting typing, antibiotic resistance detection, and epidemiological surveillance rather than delivering a direct service to the public.
- Supports pathogen surveillance by assembling genomes from clinical, environmental, and foodborne pathogen samples, enabling detection of antibiotic resistance and tracking of disease outbreaks.
- Run by
- Department of Health and Mental Hygiene (DOHMH)
- Where
- No fixed location
- Kept
- Not stated by the NYC Office of Technology and Innovation.
- Shared with
- Not stated by the NYC Office of Technology and Innovation.
- Your copy
- You cannot see the data it holds about you. What you can do
What it is for
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.
What it collects and what happens to it
Data taken in
- Raw sequencing reads (nucleotide sequence data) produced from clinical, environmental, or foodborne pathogen samples. No personal identifying information is collected or associated with this data.
Processing
Not stated by the NYC Office of Technology and Innovation.
What it does
- Spades applies de Bruijn graph algorithms to classify and assemble genomic read data into draft genome sequences. Scientists review the assembled genomes to make downstream decisions about organism typing, resistance detection, and surveillance.
Outputs
- Draft genome assemblies reconstructing the full or partial genome of the organism under analysis. These are used by laboratory scientists for organism typing, antibiotic resistance detection, and public health surveillance analyses. No personal identifying information is included in the output.
Run by
- The Department of Health and Mental Hygiene, Disease Control – Public Health Laboratory division, deploys Spades as part of its bacterial genomic analysis workflows to support public health surveillance.
Built by
Not stated by the NYC Office of Technology and Innovation.
Kept for
Not stated by the NYC Office of Technology and Innovation.
Shared with
- The genomic assembly outputs are internal laboratory data used for public health surveillance. As an individual, there is no mechanism to access these outputs, and no identifying information is collected.
Stored
Not stated by the NYC Office of Technology and Innovation.
How to read the colours
Can it identify you?
- Anonymized data
- Data about people with the link to who is broken. Stripped of identifiers, blurred, aggregated, or noised so this system can’t reasonably tie a record back to an individual.
- Pseudonymous data
- Each person’s data is tied to a token (hash, ID, template) that lets this system recognise the same person across events, but the token itself doesn’t reveal a name. Reidentification is possible with extra information.
- Identifiable data
- The data either contains a direct identifier (name, address, account name, recognisable face or voice, plate number) or carries a token this system uses to look up legal identity during processing.
Who completes the loop?
- Human decides
- This mode suggests; a person decides what to do next. The AI is always advisory — a human is in the loop on every decision. Example: a triage tool ranks cases for a clinician who chooses which to see first.
- Human executes
- This mode decides; a person carries out the result. Example: an optimizer plans the day’s trash-collection routes, and drivers run them.
- Autonomous
- This mode decides and acts on its own. No person reviews each decision or carries out the resulting action.
Definitions from the DTPR standard. Amber is about your data, violet about who decides. The fuller the shape and the deeper the colour, the more identifying the data or the less a person is involved.
- AI registerNYC Automated Decision Systems — Spades (2025)NYC Department of Health and Mental Hygiene, Disease Control – Public Health Laboratory, reported 2025.
- AI registerNYC Automated Decision Systems — Spades (2025)
- AI registerNYC Automated Decision Systems — Spades (2025)
- AI registerNYC Automated Decision Systems — Spades (2025)
- AI registerNYC Automated Decision Systems — Spades (2025)
- AI registerNYC Automated Decision Systems — Spades (2025)
- AI registerNYC Automated Decision Systems — Spades (2025)
- AI registerNYC Automated Decision Systems — Spades (2025)
- AI registerNYC Automated Decision Systems — Spades (2025)
- Register entryPublished by the NYC Office of Technology and Innovation. Reference 0fff21c3. This disclosure was drafted with AI assistance.Schema: ai@2026-05-06-beta
What you can do
Ask about this system
Questions go to the NYC Office of Technology and Innovation, not the vendor.
Your rights
- Right to Be Informed of AI UseThis tool processes only biological sample data with no personal identifying information. No individual-level decisions are made. Members of the public are not subject to automated decisions from this system and need not take action; the NYC AI use case register provides public notice of its operation.
Risks and safeguards
No risks or safeguards have been published for this system yet.