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AI agent for bioinformaticians

Reference Database Update Impact Agent

Know exactly how a reference update changes results before adopting it

AnalysisRisk managementIT and developmentScience and research
See how it worksGet access
Reference Database Update Impact Agent: what goes in, what the agent does and what you get

What it does

When a genome build, annotation or taxonomy database updates, old and new results can differ, and nobody has measured by how much. This agent notices a new release, picks a test set of past samples with known results, and reruns the pipeline on both the old and new reference versions. It compares variant calls, gene counts, taxa and filtered reads, then lists what changed and by how much. Large differences are investigated: it traces each to renamed genes, moved coordinates, or new entries. It writes a short impact note for the scientist. If the test set does not cover an important region, it adds samples and reruns. The scientist approves the upgrade. Edge case: a drop in a gene count is only a rename, so the agent maps old names to new ones first.

How it works

Follow the arrows from top to bottom. The orange dashed arrow is the loop: when a check fails, the agent goes back and tries again.

Start and resultWhat it doesA check on its own workWaits for your OKGoes back and retries
Yes, continueYes, continueApprovedNoNo 1 STARTS WHEN New reference release detected 2 DOES Read release notes and list declared changes 3 USES A TOOL Select a test set that covers key regions and sampletypes 4 USES A TOOL Run the pipeline on old and new references 5 DOES Compare calls, counts and filtered reads 6 CHECKS THE RESULT Does the test set cover the priority genes andregions? If not: add samples covering the missing regions andrerun both versions. Back to step 3. 7 USES A TOOL Trace each large difference to a rename, coordinateshift or new entry 8 CHECKS THE RESULT Is every large difference explained? If not: inspect the raw reads for unexplained cases andtest again. Back to step 7. 9 YOU APPROVE Scientist approves the upgrade or keeps the oldversion 10 RESULT Impact note with changes and decision
Read the steps as a list
  1. New reference release detected
  2. Read release notes and list declared changes
  3. Select a test set that covers key regions and sample types
  4. Run the pipeline on old and new references
  5. Compare calls, counts and filtered reads
  6. Does the test set cover the priority genes and regions?If not: add samples covering the missing regions and rerun both versions. Back to step 3.
  7. Trace each large difference to a rename, coordinate shift or new entry
  8. Is every large difference explained?If not: inspect the raw reads for unexplained cases and test again. Back to step 7.
  9. Scientist approves the upgrade or keeps the old versionThe agent waits here for your OK.
  10. Impact note with changes and decision

How it decides

It treats a difference as important when it affects more than a set share of calls or any gene on the priority list, and then traces the cause.

  • Investigate any gene whose count changes by more than 10%
  • Always check genes on the clinical or priority list
  • Match renamed genes through the release's mapping table before counting differences
  • Recommend delay when more than 2% of variant calls change without explanation

Make it yours

Every agent is a starting point. You choose these settings for your own situation.

  • Priority gene list
  • Difference threshold to investigate (default 10%)
  • Test set size and selection rule
  • Which reference sources to watch
  • Unexplained call change limit (default 2%)

What keeps you in control

It always asks you first

  • Scientist approves adopting the new reference
  • Lab lead approves rerunning already reported cases

Hard limits

  • Never overwrite old reference files
  • Never rerun reported clinical cases without lab lead approval

It stops when

  • Done: the impact note is written and the upgrade decision is recorded
  • Stop: differences stay unexplained and the version is kept

Set it up

We guide you through the set-up, step by step

Members get the full set-up guide for this agent. No technical skills needed: you copy, paste and upload.

10 minto set it up in your AI
5 AIsChatGPT, Claude, Copilot, Gemini, Grok
  • One set of instructions to paste into your AI, with the clicks for ChatGPT, Claude, Microsoft 365 Copilot, Gemini and Grok
  • The agent then walks you through connecting your own data, one source at a time
  • A downloadable copy with the flow chart, the rules and the full guide
Get access to this agent

An example run

What happensA new annotation release was tested on 24 past samples. Total gene counts differed by 1.3%, but 38 genes moved more than 10%. The agent found 30 were renames and mapped them. The remaining 8 included a priority gene whose exon list changed, so the explained check failed. After checking reads for 5 samples it confirmed the new exon was real. The scientist approved the upgrade with a note.

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