Daily agent #19: an overnight sequencing QC agent for molecular biology workflows
nlarusstone · x · 2026-11-07
Day 19 of 'an agent a day': the author builds a sequencing QC agent for molecular biology, addressing pain points like a CRO QC that got sequence counts off by a factor of 20 — work that used to need manual effort, brittle scripts, or a bioinformatics colleague.
Key elements of the sample prompt:
- Runs nightly, scanning notebook entries updated in the past day
- Finds un-QC'd sequencing results (Sanger .ab1 files or whole-plasmid reads) and aligns them to the intended sequence referenced in the entry
- For high-error nanopore reads, calls variants from the consensus across reads rather than individual reads
- Adds a short summary noting which clones match, flagging mismatches, indels, or low-quality regions
- Notes uncertainty in the entry instead of guessing when the comparison target is unclear
A concrete example of agents landing in wet-lab/bioinformatics daily workflows.
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