input: decompressed FASTQ files from Nucleus
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1. quality control (FastQC / MultiQC / VerifyBamID / QualiMap)
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2. alignment to T2T-CHM13 (BWA-MEM2 / GPU Parabricks)
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3. alignment to graph HPRC pangenome (vg giraffe / minigraph)
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4. variant calling (DeepVariant or GATK HaplotypeCaller)
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   VCF
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5. structural + copy-number variants (Manta / Lumpy / CNVnator)
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6. variant annotation + clinical databases (VEP / SnpEff / CADD / REVEL / ClinVar / PharmGKB)
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7. comparative population + ancestry analysis (PLINK / ADMIXTURE / KING / EIGENSOFT / Foldseek)
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8. evolutionary constraint & cross-species comparison (PhyloP / PhastCons / FoldSeek)
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9. predictive modeling & CRISPR design
      ├─ expression & variant effects (Enformer v2 / xTrimoGene / AlphaMissense / EVE)
      └─ edit simulation (CRISPRitz / DeepCRISPR / BE-Deep / PrimeDesign)
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10. protein structure & drug docking (ColabFold / Foldseek / AutoDock Vina)
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11. reporting dashboard (MultiQC + summary UI graphics)
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  output: complete genome interpretation: annotated variants, ancestry report, functional predictions, molecular effects, and editable targets