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AI agent for laboratory technicians

Environmental DNA Sample Pipeline Agent

Every detection is backed by passing controls at each stage, with failed batches rerun or excluded

Quality controlRisk managementScience and research
See how it worksGet access
Environmental DNA Sample Pipeline Agent: what goes in, what the agent does and what you get

What it does

Environmental DNA work is easy to contaminate, and problems often surface only after sequencing is paid for. This agent follows each sample from field collection to sequencing. At every stage it checks blanks, negative controls and positive controls: field blanks, filtration blanks, extraction blanks and PCR controls. It reads read counts and flags any blank with target DNA. If a control fails, it identifies the affected batch and requests a resample or a rerun. After reruns it rechecks the controls. The lead approves which detections go into a report. Edge case: a field blank shows traces of a fish species that appears in 3 of 40 samples, so the agent marks those 3 detections as unconfirmed.

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 Samples move to the next stage or results arrive 2 USES A TOOL Read the tracking sheet and batch records 3 USES A TOOL Read blank and control results for the stage 4 CHECKS THE RESULT Are all blanks clean and positive controlsamplified? If not: identify the affected batch and mark samples ashold. Back to step 3. 5 DOES Request a resample or rerun for held batches 6 USES A TOOL Read sequencing counts and apply detectionthresholds 7 DOES Cross-check each detection against its batch blanks 8 CHECKS THE RESULT Do reruns pass and do detections survive blankfiltering? If not: mark the detection unconfirmed and requestfurther reruns. Back to step 4. 9 DOES Draft the detection table with confidence labels 10 YOU APPROVE Lead approves which detections are reported 11 RESULT Detection report with control summary
Read the steps as a list
  1. Samples move to the next stage or results arrive
  2. Read the tracking sheet and batch records
  3. Read blank and control results for the stage
  4. Are all blanks clean and positive controls amplified?If not: identify the affected batch and mark samples as hold. Back to step 3.
  5. Request a resample or rerun for held batches
  6. Read sequencing counts and apply detection thresholds
  7. Cross-check each detection against its batch blanks
  8. Do reruns pass and do detections survive blank filtering?If not: mark the detection unconfirmed and request further reruns. Back to step 4.
  9. Draft the detection table with confidence labels
  10. Lead approves which detections are reportedThe agent waits here for your OK.
  11. Detection report with control summary

How it decides

A detection is reportable only if all blanks in its batch are clean and read counts exceed the detection threshold.

  • Hold the batch when any blank has target reads above threshold
  • Mark a detection unconfirmed if blank shows the same taxon
  • Require 2 of 3 replicates for a confirmed detection
  • Never pool results from failed batches

Make it yours

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

  • Read count threshold
  • Replicates required (default 2 of 3)
  • Blank types tracked
  • Report format

What keeps you in control

It always asks you first

  • Detections included in the report
  • Rerun or resample requests

Hard limits

  • Never reports a detection from a failed batch
  • Never overwrites raw sequence data

It stops when

  • Done: detections confirmed or labeled
  • Stop: controls fail across all batches

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 happensOf 40 pond samples, a field blank showed 180 reads of common carp, so the blank check failed. The agent held batch 2 and found 3 detections of carp in that batch. It requested resampling at those three sites. The rerun blanks were clean and 2 of 3 carp detections held up. The lead approved reporting two and left one unconfirmed.

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