{
  "accessed": "2026-08-01",
  "tools": [
    {
      "name": "samtools + bwa-mem2 + mosdepth",
      "role": "Pair-preserving alignment, fixmate/sort/markdup/index, QC and actual usable-depth measurement",
      "license": "Mixed open-source licenses; review each distribution",
      "decision": "Production plumbing baseline",
      "url": "https://www.htslib.org/"
    },
    {
      "name": "FinaleToolkit 1.0.0",
      "role": "Length, coverage, WPS, DELFI, end/breakpoint motifs, MDS and cleavage profiles from BAM/CRAM/fragments",
      "license": "MIT",
      "decision": "Primary independent feature extractor to benchmark this prototype against",
      "url": "https://epifluidlab.github.io/FinaleToolkit/documentation/cli_reference/index.html"
    },
    {
      "name": "ichorCNA",
      "role": "ULP-WGS copy-number segmentation and tumor-fraction estimate with panel of normals",
      "license": "GPL-3.0",
      "decision": "Orthogonal CNA expert and QC feature; never use its estimate as early-cancer ground truth",
      "url": "https://github.com/broadinstitute/ichorCNA"
    },
    {
      "name": "Griffin",
      "role": "Length-specific GC correction and aggregated TFBS/chromatin profiles",
      "license": "Clear BSD source text; method paper discloses patent application",
      "decision": "Primary chromatin expert after separate IP review",
      "url": "https://github.com/GavinHaLab/Griffin"
    },
    {
      "name": "FrEIA",
      "role": "Independent end-motif, length, CNA and tumor-fraction features",
      "license": "MIT",
      "decision": "Cross-implementation unit test for endpoint features",
      "url": "https://github.com/mouliere-lab/FrEIA"
    },
    {
      "name": "cfDNAPro",
      "role": "Independent Bioconductor insert-size/fragment distribution QC",
      "license": "GPL-3",
      "decision": "Orthogonal size-distribution check",
      "url": "https://bioconductor.org/packages/release/bioc/html/cfDNAPro.html"
    },
    {
      "name": "cfdnakit",
      "role": "Length-aware binning, panel of normals, CES and CNV",
      "license": "Bioconductor package terms",
      "decision": "Sensitivity-analysis comparator to ichorCNA",
      "url": "https://www.bioconductor.org/packages/release/bioc/html/cfdnakit.html"
    },
    {
      "name": "delfi3 / reproduce_lucas_wflow",
      "role": "Reference reproduction of published regional fragmentation pipelines",
      "license": "Repository-specific; verify before reuse",
      "decision": "Use to reproduce original baselines before adding corrections",
      "url": "https://github.com/cancer-genomics/delfi3"
    },
    {
      "name": "LIONHEART",
      "role": "Cross-dataset open-chromatin correlation expert",
      "license": "Code open; shared models/resources explicitly research/noncommercial",
      "decision": "Strong external comparator, not an unrestricted product dependency",
      "url": "https://github.com/BesenbacherLab/lionheart"
    },
    {
      "name": "DNABERT-2",
      "role": "Frozen generic DNA fragment embedding benchmark",
      "license": "Apache-2.0",
      "decision": "First foundation-model comparator only after classical baseline lock",
      "url": "https://github.com/MAGICS-LAB/DNABERT_2"
    },
    {
      "name": "Caduceus",
      "role": "Reverse-complement-aware frozen DNA fragment embedding benchmark",
      "license": "Apache-2.0",
      "decision": "Second generic foundation-model comparator",
      "url": "https://github.com/kuleshov-group/caduceus"
    },
    {
      "name": "LEAF-1",
      "role": "Cleavage-boundary-aware fragment foundation model plus MIL",
      "license": "PolyForm Noncommercial / preprint resource terms",
      "decision": "Best research benchmark after license acceptance; not MVP dependency",
      "url": "https://github.com/csglab/leaf-1"
    }
  ]
}