{
  "assemblies": [
    {
      "name": "grape",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "grape-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_145_Genoscope.12X.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_145_Genoscope.12X.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_145_Genoscope.12X.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "peach",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "peach-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.0.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.0.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.0.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "SyntenyTrack",
      "trackId": "grape_peach_synteny_mcscan",
      "name": "Grape peach synteny (MCScan, anchors)",
      "assemblyNames": ["peach", "grape"],
      "category": ["Annotation"],
      "adapter": {
        "type": "MCScanAnchorsAdapter",
        "mcscanAnchorsLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape.peach.anchors.gz"
        },
        "bed1Location": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/grape.bed.gz"
        },
        "bed2Location": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/peach.bed.gz"
        },
        "assemblyNames": ["grape", "peach"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "grape_peach_synteny_mcscan_simple",
      "name": "Grape peach synteny (MCScan, simple anchors)",
      "assemblyNames": ["peach", "grape"],
      "category": ["Annotation"],
      "adapter": {
        "type": "MCScanSimpleAnchorsAdapter",
        "mcscanSimpleAnchorsLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/grape.peach.anchors.simple.gz"
        },
        "bed1Location": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/grape.bed.gz"
        },
        "bed2Location": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/peach.bed.gz"
        },
        "assemblyNames": ["grape", "peach"]
      }
    },

    {
      "trackId": "grape_peach_nucmer",
      "type": "SyntenyTrack",
      "name": "Grape vs Peach (nucmer)",
      "assemblyNames": ["peach", "grape"],
      "adapter": {
        "type": "DeltaAdapter",
        "deltaLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/out1.delta.gz",
          "locationType": "UriLocation"
        },
        "assemblyNames": ["peach", "grape"]
      }
    },

    {
      "trackId": "grape_peach_paf",
      "type": "SyntenyTrack",
      "name": "Grape vs Peach (PAF)",
      "assemblyNames": ["peach", "grape"],
      "metadata": {
        "command": "minimap2 -c Vvinifera_145_Genoscope.12X.fa Ppersica_298_v2.0.fa > out.paf",
        "version": "2.24-r1122"
      },
      "adapter": {
        "type": "PAFAdapter",
        "pafLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/peach_grape.paf.gz",
          "locationType": "UriLocation"
        },
        "assemblyNames": ["peach", "grape"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "dotplot_track_small",
      "name": "Grape vs peach small (PAF)",
      "assemblyNames": ["grape", "peach"],
      "adapter": {
        "type": "PAFAdapter",
        "pafLocation": {
          "uri": "peach_grape_small.paf.gz",
          "locationType": "UriLocation"
        },
        "assemblyNames": ["peach", "grape"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "dotplot_track_small_cigar",
      "name": "Grape vs peach small (PAF w/ CIGAR)",
      "assemblyNames": ["grape", "peach"],
      "adapter": {
        "type": "PAFAdapter",
        "pafLocation": {
          "uri": "peach_grape_small_cigar.paf.gz",
          "locationType": "UriLocation"
        },
        "assemblyNames": ["peach", "grape"]
      }
    },

    {
      "type": "FeatureTrack",
      "trackId": "grape_genes",
      "name": "Vvinifera_457_v2.1.gene.sorted.gff",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_457_v2.1.gene.sorted.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_457_v2.1.gene.sorted.gff.gz.tbi"
          }
        }
      },
      "assemblyNames": ["grape"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "peach_genes",
      "name": "Ppersica_298_v2.1.gene.sorted.gff3",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.1.gene.sorted.gff3.gz"
        },
        "index": {
          "location": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.1.gene.sorted.gff3.gz.tbi"
          }
        }
      },
      "assemblyNames": ["peach"]
    }
  ],
  "defaultSession": {
    "name": "Grape vs Peach (small)",
    "views": [
      {
        "id": "MiDMyyWpp",
        "type": "DotplotView",
        "assemblyNames": ["peach", "grape"],
        "hview": {
          "displayedRegions": [],
          "bpPerPx": 100000,
          "offsetPx": 0
        },
        "vview": {
          "displayedRegions": [],
          "bpPerPx": 100000,
          "offsetPx": 0
        },
        "tracks": [
          {
            "type": "SyntenyTrack",
            "configuration": "dotplot_track_small",
            "displays": [
              {
                "type": "DotplotDisplay",
                "configuration": "dotplot_track_small-DotplotDisplay"
              }
            ]
          }
        ],
        "displayName": "Grape vs Peach dotplot"
      }
    ]
  }
}
