example	analysis_type	dataset	inputs	design_or_truth	pipeline	primary_endpoints	validation_surface
Airway	rnaseq_expression	GSE52778	8 paired-end RNA-seq libraries from four donors	DESeq2 design ~ donor + condition; frozen GEO Dex-versus-untreated table	STAR; featureCounts; DESeq2	log2FC rank correlation; direction concordance; preregistered sentinel directions	execution plan; run summary; standard tables; validate-result; comparison table
ST93 MRSA	wgs_bacteria	PRJNA286158	6 paired-end bacterial WGS isolates	Published ST93/MRSA identity	fastp; SPAdes; Prokka; MLST; AMRFinderPlus	ST93 concordance; mecA recovery and sequence agreement	execution plan; run summary; standard tables; validate-result
ST93 MRSA SNP comparison	wgs_bacteria (strict external tracks)	PRJNA286158 + PRJEB3144 + PRJNA232112	81 MD5-verified ENA read sets (six study isolates plus paper context cohorts)	Published six-isolate pairwise SNP range 7-60 (mean 44) against JKD6159 CP002114	paper_spandx: SPANDx v2.6 default; abi_bcftools: BWA mem + samtools + bcftools haploid joint calling	Six-isolate pairwise SNP range recovery; side-by-side track comparison	literature endpoint table; pairwise distance tables; track comparison summary; provenance; SHA256SUMS
SCAPP plasmidome	metagenomic_plasmid	SRR11038083	18.6 million paired-end read pairs	PLSDB 2018-12-05 plus paper-method two-stage coverage reconstruction	QC; metagenome assembly; plasmid detection/consensus; Bakta; MOB-suite; AMR tools	independent paper-method precision/recall/F1 after truth gate; auxiliary structural and mobility evidence	checksummed inputs; execution provenance; per-plasmid evidence; machine evidence JSON