VERIFIED INPUT CONTRACT
MultiQC compatibility evidence
Verified 7 September 2026 · GenomQC parser 1.1.1-beta
Compatibility means that GenomQC can map documented fields and units. It does not validate scientific thresholds or guarantee that the mapped metrics are appropriate for a particular experiment.
Verified formats
- MultiQC 1.35
multiqc_data.json, usingreport_general_stats_data. - MultiQC 1.35
multiqc_general_stats.txt. - CSV or TSV with a sample column and at least two recognized metrics for every sample.
Mapped metrics
- Reads: passed/after-filtering reads when available, then before-filtering or total reads.
- Q30: after-filtering Q30 rate and documented Q30 percentage fields. Q30 base counts are not interpreted as percentages.
- GC: after-filtering GC content and documented GC percentage fields.
- Duplication: fastp duplication and FastQC percent duplicates.
- Adapter: fastp adapter percentage and documented adapter percentage/content fields.
- Retention: fastp surviving reads/bases and documented retention percentage fields.
Unit handling
MultiQC general-statistics TSV read counts displayed in millions are converted back to counts. MultiQC JSON fastp Q30 rate and GC content fractions are converted to percentage points. Fields named pct_adapter, pct_duplication and pct_surviving_* already contain percentage points and are not multiplied again. In custom CSV/TSV files, percentage columns must use 0–100 values; an explicit percent sign is accepted, so 0.5% means 0.5 percentage points.
Fail-closed behavior
Blank, NA, null and non-numeric values remain missing; they are never converted to zero. GenomQC stops the decision run if any detected sample has fewer than two recognized metrics. A PASS result only means that no available mapped value crossed the active rule boundaries.
Reproducible fixture
The automated fixture was produced with MultiQC 1.35 from the official MIT-licensed MultiQC test-data repository: fastp SAMPLE.json object 0485df3a9a49bd158346926e4a8ff9112de2f0b7 and FastQC fastqc_data.txt object ea3268141118fc4ad042bebd0c30090315fc649c. The fixture is compatibility evidence, not a biological validation dataset or customer case study.
Inspect the upstream test-data repository · Inspect the GenomQC fixture and tests
Need another export layout?
Request a metadata-only compatibility check. Share the MultiQC version, export filename, column names and approximate sample count first. Do not email raw reads, patient information or sensitive research content.