{
  "assemblies": [
    {
      "name": "T2T_chrY",
      "displayName": "chrY (T2T-CHM13v2)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "T2T_chrY-refseq",
        "adapter": {
          "type": "TwoBitAdapter",
          "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit",
          "chromSizes": "chrY.chrom.sizes"
        }
      },
      "refNameAliases": { "uri": "chrY.aliases.txt" }
    },
    {
      "name": "T2T_chrY_self",
      "displayName": "chrY (T2T-CHM13v2)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "T2T_chrY_self-refseq",
        "adapter": {
          "type": "TwoBitAdapter",
          "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit",
          "chromSizes": "chrY.chrom.sizes"
        }
      },
      "refNameAliases": { "uri": "chrY.aliases.txt" }
    }
  ],
  "tracks": [
    {
      "type": "SyntenyTrack",
      "trackId": "hs1_chrY_self",
      "name": "chrY self-alignment (minimap2)",
      "assemblyNames": ["T2T_chrY_self", "T2T_chrY"],
      "metadata": {
        "command": "minimap2 -x asm20 -P chrY.fa chrY.fa, over chrY:2,700,000-26,600,000",
        "note": "-P is required: without it minimap2 marks every off-diagonal hit secondary and drops it"
      },
      "adapter": {
        "type": "PairwiseIndexedPAFAdapter",
        "assemblyNames": ["T2T_chrY_self", "T2T_chrY"],
        "uri": "https://jbrowse.org/demos/scratch/hs1_chrY_self.pif.gz",
        "csi": true
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hs1_chrY_genes",
      "name": "NCBI RefSeq genes (hs1)",
      "assemblyNames": ["T2T_chrY", "T2T_chrY_self"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "https://jbrowse.org/ucsc/hs1/hs1.gff.gz",
        "csi": true
      }
    }
  ]
}