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Methods

Select a QC scheme to view its specific methods and notes.

  • qualibact-v1.0

    Species-specific thresholds derived from AllTheBacteria (2.4M genomes) and RefSeq complete genomes using Isolation Forest outlier detection.

  • qualibact-v1.1

    Refined thresholds incorporating additional genome sets beyond AllTheBacteria, with species-specific adjustments to qualibact-v1.0 criteria.

  • REFSEQ-QC-v1

    Quality control of NCBI RefSeq reference genomes using simulated short reads, Shovill assembly, and CheckM2 completeness/contamination checks.

  • enterobase-v2.3

    Third-party assembly-QC cutoffs from the EnteroBase QA pipeline (Zhou et al., 2020). Genus-level, single-tier (FAIL only), applied only to species EnteroBase actively curates. Surfaced for side-by-side comparison; never the preferred scheme.