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AI agent for microbiologists

Microbial Genome Assembly QC Agent

Only good assemblies used for typing and resistance calls

Quality controlScience and researchHealthcare
See how it worksGet access
Microbial Genome Assembly QC Agent: what goes in, what the agent does and what you get

What it does

Whole genome sequencing of isolates is routine, but every assembly needs checking before results are reported. This agent runs read QC and assembly, then checks coverage, contig count, genome size, completeness and contamination against expected values for the species. Assemblies that fail are re-run with different settings, and if they still fail, flagged for resequencing. Passing assemblies get typing and resistance gene calls. The agent then compares those calls with the lab's phenotype results, such as susceptibility tests, and flags any disagreement for a scientist to review. It produces a QC summary per isolate. You approve every result before it is reported. Edge case: two species detected in one sample is flagged as a mixed culture, and the sample is sent back for re-isolation instead of being assembled.

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, continueApprovedNo 1 STARTS WHEN Sequencing run finishes 2 USES A TOOL Run read QC and assembly 3 DOES Check coverage, size, completeness and contamination 4 CHECKS THE RESULT Does the assembly pass QC? If not: re-run or flag for resequencing. Back to step 2. 5 USES A TOOL Run typing and resistance gene calls 6 YOU APPROVE Microbiologist approves reporting 7 RESULT Results stored
Read the steps as a list
  1. Sequencing run finishes
  2. Run read QC and assembly
  3. Check coverage, size, completeness and contamination
  4. Does the assembly pass QC?If not: re-run or flag for resequencing. Back to step 2.
  5. Run typing and resistance gene calls
  6. Microbiologist approves reportingThe agent waits here for your OK.
  7. Results stored

How it decides

It passes assemblies meeting coverage, size, completeness and contamination limits.

  • Flag mixed cultures
  • Re-run with alternate settings
  • Use species-specific limits

Make it yours

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

  • QC limits
  • Pipeline settings
  • Databases
  • Report format

What keeps you in control

It always asks you first

  • Reporting results

Hard limits

  • Never deletes raw reads

It stops when

  • Done: results stored
  • Stop: run failed

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 run finished on April 3 with 24 Salmonella isolates. Twenty-one assemblies passed. Isolate S-2214 had 412 contigs and a genome size of 5.9 Mb against an expected 4.8, a sign of contamination. The agent went back, reran with stricter read trimming, and it still failed, so it flagged the isolate for resequencing. Two others passed after a rerun. The microbiologist approved reporting typing and resistance results for 23 isolates.

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