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AI-Assisted Genomic Sequence Alignment for Public Health

What it is for

Research & Development
  • BWA is used for Legionella and PulseNet sequencing analyses to support public health disease outbreak investigations. It is deployed 1–2 times per week in a supervised laboratory workflow.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

Environmental Health
  • The system supports environmental health surveillance by identifying and comparing genomic sequences from pathogens such as Legionella, contributing to outbreak detection and public health response.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

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
Accountable organization
Your copy
You cannot see the data it holds about you. What you can do

What it is for

Research & DevelopmentEnvironmental Health

This tool aligns DNA sequencing data from biological samples to a reference genome, helping public health scientists detect and compare bacterial strains such as Legionella. It is used by the NYC Department of Health and Mental Hygiene's Public Health Laboratory to support disease outbreak investigations. No identifying personal information is collected or used — the system works on biological sample data only, not data tied to named individuals.

What it collects and what happens to it

Data taken in

About a measurement
Anonymized data
  • Laboratory-generated sequencing reads (short genomic sequences produced by Illumina sequencers from biological samples) and an organism-specific reference genome selected for the public health investigation. No identifying personal information is collected or disclosed.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

Operational data
Anonymized data
  • An organism-specific reference genome selected for the public health investigation. This is curated biological reference data, not individual patient data.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

Processing

Classification & Prediction
  • BWA uses Burrows-Wheeler transformations to align short sequencing reads to a reference genome. It is optimal for low-divergent genomic data and short read data such as Illumina sequence data. The algorithm predicts the most probable positional mapping for each fragment against the reference.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

What it does

Deciding (Analytical AI)
Human decides
  • BWA scores and ranks the alignment of sequencing reads against a reference genome, producing similarity and variation data. Autonomy is supervised — public health scientists review alignments and make investigative conclusions.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

Outputs

About a measurement
Anonymized data
  • Read-to-reference alignments showing genomic similarity and variation, used for variant detection and comparison in Legionella and PulseNet sequencing analyses. Output is not linked to named individuals.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

A recommendation or prediction
Anonymized data
  • Alignment outputs support downstream variant detection and comparative genomics, effectively acting as an advisory input into public health outbreak investigation decisions made by scientists.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

Run by

Department of Health and Mental Hygiene (DOHMH)
  • The NYC Department of Health and Mental Hygiene's Public Health Laboratory deploys BWA to align genomic sequencing data for Legionella and PulseNet analyses as part of public health disease investigation workflows.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

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

Not available to me
  • BWA processes biological samples and produces genomic alignment data. This data is not linked to named individuals and is not accessible to the general public. Output is used internally by Public Health Laboratory scientists.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

Available to the accountable organization
  • Alignment output data is available to the NYC Department of Health and Mental Hygiene's Public Health Laboratory for disease investigation purposes.

NYC Automated Decision Systems — Burrows-Wheeler Aligner (BWA)

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.

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 Algorithmic TransparencyBWA is open-source software available at https://github.com/lh3/bwa. The algorithmic logic — Burrows-Wheeler transformation for genomic alignment — is publicly documented. As no personal identifying information is processed, individual data rights such as access or correction are not directly applicable.

Risks and safeguards

No risks or safeguards have been published for this system yet.