{
  "assemblies": [
    {
      "name": "tauschii",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "tauschii-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "tauschii.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "wheat",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "wheat-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "wheat.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "durum",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "durum-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "durum.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "emmer",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "emmer-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "emmer.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "urartu",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "urartu-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "urartu.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "timopheevii",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "timopheevii-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "timopheevii.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "NcbiSequenceReportAliasAdapter",
          "location": {
            "uri": "timopheevii.sequence_report.tsv",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "configuration": {},
  "connections": [],
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    "name": "Wheat orthology synteny",
    "views": [
      {
        "type": "LinearSyntenyView",
        "displayName": "tauschii - wheat - durum - emmer - urartu - timopheevii (OrthoFinder orthogroups)",
        "views": [
          {
            "assembly": "tauschii"
          },
          {
            "assembly": "wheat"
          },
          {
            "assembly": "durum"
          },
          {
            "assembly": "emmer"
          },
          {
            "assembly": "urartu"
          },
          {
            "assembly": "timopheevii"
          }
        ],
        "tracks": [
          ["wheat_orthogroups"],
          ["wheat_orthogroups"],
          ["wheat_orthogroups"],
          ["wheat_orthogroups"],
          ["wheat_orthogroups"]
        ],
        "color": { "field": "reference" },
        "autoDiagonalize": true,
        "sameScale": true,
        "collapseEmptyRows": true
      }
    ]
  },
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "tauschii_genes",
      "name": "tauschii genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "tauschii.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "tauschii.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["tauschii"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "wheat_genes",
      "name": "wheat genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "wheat.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "wheat.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
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    },
    {
      "type": "FeatureTrack",
      "trackId": "durum_genes",
      "name": "durum genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "durum.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "durum.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["durum"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "emmer_genes",
      "name": "emmer genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "emmer.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "emmer.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["emmer"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "urartu_genes",
      "name": "urartu genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
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          "locationType": "UriLocation"
        },
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            "uri": "urartu.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["urartu"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "timopheevii_genes",
      "name": "timopheevii genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "timopheevii.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "timopheevii.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["timopheevii"]
    },
    {
      "type": "SyntenyTrack",
      "trackId": "wheat_orthogroups",
      "name": "Wheat orthogroups (OrthoFinder)",
      "assemblyNames": [
        "tauschii",
        "wheat",
        "durum",
        "emmer",
        "urartu",
        "timopheevii"
      ],
      "adapter": {
        "type": "MCScanBlocksAdapter",
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        "blockAssemblies": [
          "durum",
          "emmer",
          "tauschii",
          "timopheevii",
          "urartu",
          "wheat"
        ],
        "bedLocations": [
          {
            "uri": "durum.bed.gz"
          },
          {
            "uri": "emmer.bed.gz"
          },
          {
            "uri": "tauschii.bed.gz"
          },
          {
            "uri": "timopheevii.bed.gz"
          },
          {
            "uri": "urartu.bed.gz"
          },
          {
            "uri": "wheat.bed.gz"
          }
        ],
        "assemblyNames": [
          "tauschii",
          "wheat",
          "durum",
          "emmer",
          "urartu",
          "timopheevii"
        ]
      }
    }
  ]
}