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QualiBact Integration

speccheck can refresh criteria from the machine-readable QualiBact export:

https://static.qualibact.org/api/v2/thresholds.csv

Current behavior

  • thresholds are downloaded from the aggregate CSV export
  • each species follows the QualiBact index preferred_scheme
  • supported metrics are mapped into the internal speccheck criteria format
  • Total_Coding_Sequences is mapped when final bounds are present
  • existing unmanaged criteria rows are preserved
  • optional compatibility mode adds species-aware, pinned PASS/WARN/FAIL tier columns

QualiBact thresholds are calibrated around CheckM2-derived metrics. In speccheck outputs these still use the historical Checkm.* column prefix for compatibility, but the supported fields are CheckM2-style fields such as Completeness, Contamination, Genome_Size, GC_Content, Contig_N50, Total_Contigs, and Total_Coding_Sequences. Native CheckM1 tabular reports are also accepted and normalised to these canonical fields; marker-lineage-only fields are not used as QualiBact metrics.

Supported imported metrics

  • Genome_Size
  • N50
  • no_of_contigs
  • GC_Content
  • Completeness
  • Contamination
  • Total_Coding_Sequences

QualiBact tier compatibility

All Speccheck criteria use the same PASS/WARN/FAIL vocabulary. summary can additionally apply the release-pinned preferred QualiBact scheme for the species assigned to each sample:

speccheck summary qc_results \
  --output qc_report \
  --plot \
  --qualifyr-style \
  --qualibact-compat

This adds:

  • qualibact_qc: PASS, WARN, FAIL, or NOT_EVALUATED
  • qualibact_compat_reasons: threshold reasons such as no_of_contigs >670.0
  • qualibact_compat_source: pinned source label

Each release pins the aggregate threshold snapshot and preferred-scheme map for reproducibility. The E. coli case-study scheme is:

https://static.qualibact.org/static/species/Escherichia_coli/qualibact-v1.0

Speccheck applies this E. coli threshold set to samples assigned to the genus Shigella. The reported species assignment is retained, and the compatibility source records that E. coli thresholds were applied to that Shigella species.

QualiBact WARN remains WARN in both qualibact_qc and overall_qc. Speccheck does not silently convert warnings into failures.

Historical qualibact_tier and qualibact_reasons input values are emitted as historical_qualibact_qc and comparison reasons. They are comparison metadata. They do not define overall_qc and do not replace freshly computed compatibility reasons. This separation prevents older assemblies or exports from silently overriding the current QC verdict.

The completed 100-sample case study found 73% exact tier agreement: 68/70 historical PASS, 1/20 historical WARN, and 4/10 historical FAIL remained in the same tier. Three samples were NOT_EVALUATED because their current species could not be identified. These are concordance results, not sensitivity or specificity, because historical tiers are not treated as ground truth.

Regression fixtures

Pinned E. coli fixtures are kept under tests/qualibact/:

  • thresholds_subset.csv
  • ecoli_pass_subset.csv
  • ecoli_fail_subset.csv

These support deterministic tests for importer behaviour and report generation. Boundary tests verify that exact FINAL and WARN limits use QualiBact's inclusive semantics. A WARN side is ignored when no corresponding FINAL side exists, because that side has no defined FAIL region.