{
  "plugins": [
    {
      "name": "GraphGenomeView",
      "esmUrl": "https://jbrowse.org/plugins/jbrowse-plugin-graphgenomeviewer/latest/dist/jbrowse-plugin-graphgenomeviewer.esm.js"
    }
  ],
  "assemblies": [
    {
      "name": "hg38",
      "aliases": ["GRCh38"],
      "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz",
      "refNameAliases": {
        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
      },
      "cytobands": {
        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/cytoBand.txt"
      }
    },
    {
      "name": "hs1",
      "displayName": "Human (T2T-CHM13v2.0/hs1)",
      "aliases": ["CHM13", "T2T-CHM13v2.0"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "hs1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "uri": "hs1.chrom.sizes"
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "hg38_ncbiRefSeq_ucsc",
      "name": "NCBI RefSeq genes (hg38)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz",
        "csi": true
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hs1_ncbiRefSeq_ucsc",
      "name": "NCBI RefSeq genes (hs1)",
      "assemblyNames": ["hs1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "https://jbrowse.org/ucsc/hs1/hs1.gff.gz",
        "csi": true
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_minigraph_bubbles",
      "name": "HPRC release 2 bubbles",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "MinigraphBubbleAdapter",
        "uri": "https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.bubbles.bed.gz",
        "assemblyNameToPanSN": {
          "hg38": "GRCh38"
        }
      },
      "displayDefaults": {
        "color": "rgb(130,130,130)"
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "hprc_minigraph_alleles",
      "name": "HPRC release 2 graph: allele inventory",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.alleles.bed.gz"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hprc2_wave_grch38",
      "name": "HPRC release 2 phased VCF, vcfwave-decomposed (464 haplotypes)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.wave.vcf.gz"
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "displayId": "hprc2_wave_grch38_regular",
          "unit": "haplotype"
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "hprc2_pgbi_grch38",
      "name": "HPRC release 2 phased VCF, one record per allele (462 haplotypes)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.pgbi.vcf.gz",
        "fetchSizeLimit": 20000000
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "displayId": "hprc2_pgbi_grch38_regular",
          "unit": "haplotype"
        }
      ]
    },
    {
      "type": "GraphTrack",
      "trackId": "hprc_minigraph_segments",
      "name": "HPRC v2.1 graph (rGFA segments)",
      "assemblyNames": ["hg38", "hs1"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.anchored",
        "assemblyNameToPanSN": {
          "hg38": "GRCh38",
          "hs1": "CHM13"
        },
        "coarse": {
          "uri": "https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.fold10000",
          "aboveBpPerPx": 1000
        }
      },
      "displayDefaults": {
        "color": {
          "field": "rank",
          "scale": "threshold",
          "domain": ["1"],
          "range": ["rgb(52,152,219)", "rgb(237,137,44)"],
          "labels": ["reference", "other assemblies"],
          "title": "Segment rank"
        }
      },
      "displays": [
        {
          "type": "LinearGraphDisplay",
          "displayId": "hprc_minigraph_segments-LinearGraphDisplay"
        },
        {
          "type": "LinearBasicDisplay",
          "displayId": "hprc_minigraph_segments-LinearBasicDisplay"
        }
      ]
    },
    {
      "type": "GraphTrack",
      "trackId": "hprc_v2_1_walks_hs1",
      "name": "HPRC v2.1 haplotype walks",
      "assemblyNames": ["hs1"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "walksUri": "https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f2.CHM13",
        "assemblyNameToPanSN": {
          "hs1": "CHM13"
        },
        "defaultHaplotypes": [
          "HG00097#1",
          "HG00099#1",
          "HG00128#1",
          "HG00133#1",
          "HG01109#1",
          "HG01123#1",
          "HG01960#1",
          "HG02055#1"
        ]
      },
      "displays": [
        {
          "type": "LinearGraphDisplay",
          "displayId": "hprc_v2_1_walks_hs1-LinearGraphDisplay"
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_curated_vntrs",
      "name": "Curated VNTRs (LPA KIV-2)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "BedAdapter",
        "uri": "https://jbrowse.org/demos/hprc/hprc_curated_vntrs.bed",
        "columnNames": ["chrom", "chromStart", "chromEnd", "name", "period"]
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg38_cytobands_ucsc",
      "name": "Cytogenetic bands (hg38)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/cytoBand.bed.gz",
        "csi": true,
        "columnNames": ["refName", "start", "end", "name", "gieStain"]
      }
    }
  ]
}
