Not all QC failures are equal. A WGS run where on-target alignment is 97% instead of 98% is a different situation from one where it is 62%. A differential expression analysis where the principal component plot shows a clear technical batch effect is a different situation from one with moderate within-group variation. BioMate's three-tier grading system gives you a calibrated, evidence-based assessment of where your results sit — with the detail to act on it.
The Problem With Binary Pass/Fail
Binary QC is seductive because it seems clear-cut. Either a run passes or it does not. But binary assessment discards the information that matters most: how far outside the threshold a failing metric is, which specific metric drove the result, and whether the deviation is clinically or scientifically meaningful in context.
A result flagged as "failed" by a binary system might be perfectly acceptable for a discovery screen but unacceptable for a clinical diagnostic. A result that passes binary QC but sits just inside every threshold simultaneously may represent a lower-quality dataset than one that fails on one metric but exceeds all others substantially. Binary QC cannot express these distinctions.
Evidence-Graded Thresholds
BioMate's QC profiles are built from published community guidelines. For genomics, this means ENCODE, GATK, and GATK best practices. For cryo-EM, the field's consensus resolution and particle statistics criteria. For pharmacokinetics, ICH guidance on model validation. For ADMET, the medicinal chemistry literature on accepted threshold ranges by therapeutic area and route.
Each QC criterion has three bands. GOLD corresponds to the threshold that the relevant guideline identifies as the mark of a high-quality dataset for that method. SILVER corresponds to acceptable quality for most research applications, with known limitations that are documented in the report. BRONZE corresponds to below the SILVER threshold — usable in some contexts with caveats, but requiring explicit justification if used to support a primary conclusion.
"BRONZE is better than silence. A transparent assessment of a below-threshold result is always more useful than a system that passes everything and leaves interpretation to the researcher."
What Each Grade Tells You
A GOLD grade means the result meets the quality bar the community uses for high-confidence publication. A SILVER grade means the result is acceptable for most research purposes with the documented caveats noted. A BRONZE grade means a specific metric — identified by name and value in the report — fell below the SILVER threshold, the auto-QC loop exhausted available remediation options, and the result should be interpreted with the documented limitation in mind.
Further reading: ENCODE experiment guidelines, GTEx portal (Genotype-Tissue Expression project), MultiQC quality control aggregator, and nf-core community pipeline standards.
Every result you receive from BioMate comes with a grade and a rationale — not just a number. You can share the QC report with collaborators, attach it to a data submission, or include it in a Methods section with confidence that the quality assessment is traceable to published standards.