{
  "assemblies": [
    {
      "name": "K12",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "K12-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "K12.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "K12.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "K12.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "Sakai",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Sakai-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "Sakai.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "Sakai.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "Sakai.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "CFT073",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "CFT073-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "CFT073.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "CFT073.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "CFT073.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "NCTC86",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "NCTC86-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "NCTC86.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "NCTC86.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "NCTC86.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "IAI39",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "IAI39-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "IAI39.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "IAI39.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "IAI39.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "configuration": {},
  "connections": [],
  "defaultSession": {
    "name": "E. coli pangenome graph",
    "views": [
      {
        "type": "LinearSyntenyView",
        "init": {
          "views": [
            {
              "assembly": "K12"
            },
            {
              "assembly": "Sakai"
            },
            {
              "assembly": "CFT073"
            },
            {
              "assembly": "NCTC86"
            },
            {
              "assembly": "IAI39"
            }
          ],
          "tracks": [
            ["ecoli_pggb_ava"],
            ["ecoli_pggb_ava"],
            ["ecoli_pggb_ava"],
            ["ecoli_pggb_ava"]
          ],
          "drawCurves": false,
          "minAlignmentLength": 10000
        }
      },
      {
        "type": "LinearGenomeView",
        "init": {
          "assembly": "K12",
          "loc": "chr:1,000,000-1,010,000",
          "tracks": [
            "K12_genes",
            "ecoli_pggb_depth",
            "ecoli_pggb_carriage",
            "ecoli_pggb_pav",
            "ecoli_pggb_variants",
            "ecoli_pggb_maf"
          ]
        }
      }
    ]
  },
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "K12.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "K12.gff.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "assemblyNames": ["K12"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "Sakai_genes",
      "name": "Sakai genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "Sakai.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "Sakai.gff.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "assemblyNames": ["Sakai"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "CFT073_genes",
      "name": "CFT073 genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "CFT073.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "CFT073.gff.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "assemblyNames": ["CFT073"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "NCTC86_genes",
      "name": "NCTC86 genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "NCTC86.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "NCTC86.gff.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "assemblyNames": ["NCTC86"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "IAI39_genes",
      "name": "IAI39 genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "IAI39.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "IAI39.gff.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "assemblyNames": ["IAI39"]
    },
    {
      "type": "SyntenyTrack",
      "trackId": "ecoli_ava",
      "name": "E. coli pangenome (all-vs-all PAF)",
      "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
      "adapter": {
        "type": "AllVsAllPAFAdapter",
        "pafLocation": {
          "uri": "all_vs_all.paf.gz",
          "locationType": "UriLocation"
        },
        "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "ecoli_pggb_ava",
      "name": "pggb graph: all-vs-all synteny (wfmash)",
      "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
      "adapter": {
        "type": "AllVsAllIndexedPAFAdapter",
        "pifGzLocation": {
          "uri": "ecoli_pggb_ava.pif.gz"
        },
        "index": {
          "location": {
            "uri": "ecoli_pggb_ava.pif.gz.tbi"
          }
        },
        "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "ecoli_pggb_untangle",
      "name": "pggb graph: synteny from the graph (odgi untangle)",
      "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
      "adapter": {
        "type": "AllVsAllIndexedPAFAdapter",
        "pifGzLocation": {
          "uri": "ecoli_pggb_untangle.pif.gz"
        },
        "index": {
          "location": {
            "uri": "ecoli_pggb_untangle.pif.gz.tbi"
          }
        },
        "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_untangle_rows",
      "name": "pggb graph: untangle per strain (orientation, vs K12)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "ecoli_pggb_untangle_rows.bed.gz"
      },
      "displays": [
        {
          "type": "LinearMultiRowFeatureDisplay",
          "partitionField": "strain",
          "rowOrder": ["Sakai", "CFT073", "NCTC86", "IAI39"],
          "legend": [
            { "label": "Same orientation as K12", "color": "rgb(153,153,153)" },
            { "label": "Inverted", "color": "rgb(214,39,40)" }
          ]
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "ecoli_pggb_variants",
      "name": "pggb graph: pangenome variants (vs K12)",
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "ecoli_pggb.vcf.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "ecoli_pggb.vcf.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "assemblyNames": ["K12"]
    },
    {
      "type": "VariantTrack",
      "trackId": "ecoli_pggb_snarls",
      "name": "pggb graph: raw snarl tree (nested, vs K12)",
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "ecoli_pggb_snarls.vcf.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "ecoli_pggb_snarls.vcf.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "assemblyNames": ["K12"]
    },
    {
      "type": "MafTrack",
      "trackId": "ecoli_pggb_maf",
      "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "MafTabixAdapter",
        "samples": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
        "nhLocation": {
          "uri": "ecoli_pggb.nh"
        },
        "uri": "ecoli_pggb.maf.bed.gz"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "ecoli_pggb_depth",
      "name": "pggb graph: pangenome depth (paths over K12)",
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "ecoli_pggb_depth.bw",
          "locationType": "UriLocation"
        }
      },
      "assemblyNames": ["K12"]
    },
    {
      "type": "MultiQuantitativeTrack",
      "trackId": "ecoli_pggb_pav",
      "name": "pggb graph: per-strain presence (odgi pav, vs K12)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "MultiWiggleAdapter",
        "subadapters": [
          {
            "type": "BigWigAdapter",
            "name": "Sakai",
            "bigWigLocation": {
              "uri": "ecoli_pggb_pav_Sakai.bw"
            }
          },
          {
            "type": "BigWigAdapter",
            "name": "CFT073",
            "bigWigLocation": {
              "uri": "ecoli_pggb_pav_CFT073.bw"
            }
          },
          {
            "type": "BigWigAdapter",
            "name": "NCTC86",
            "bigWigLocation": {
              "uri": "ecoli_pggb_pav_NCTC86.bw"
            }
          },
          {
            "type": "BigWigAdapter",
            "name": "IAI39",
            "bigWigLocation": {
              "uri": "ecoli_pggb_pav_IAI39.bw"
            }
          }
        ]
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_minigraph_segments",
      "name": "minigraph graph: rGFA segments (browsable by locus)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "ecoli_minigraph"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_minigraph_paths",
      "name": "minigraph graph: per-strain path through each bubble",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "ecoli_minigraph_paths.bed.gz"
      },
      "displays": [
        {
          "type": "LinearMultiRowFeatureDisplay",
          "partitionField": "strain",
          "lengthField": "delta",
          "rowOrder": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
          "legend": [
            {
              "label": "reference path",
              "color": "rgb(204,204,204)"
            },
            {
              "label": "insertion",
              "color": "rgb(192,0,192)"
            },
            {
              "label": "deletion",
              "color": "rgb(128,128,128)"
            },
            {
              "label": "same length, different path",
              "color": "rgb(0,154,138)"
            },
            {
              "label": "no call",
              "color": "rgb(191,170,64)"
            }
          ]
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "ecoli_minigraph_alleles",
      "name": "minigraph graph: allele inventory (from the rGFA alone)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "ecoli_minigraph.alleles.bed.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_subgraph_nodes",
      "name": "pggb subgraph: nodes on K12, colored by depth",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "ecoli_pggb_subgraph_nodes.bed.gz",
        "columnNames": [
          "chrom",
          "start",
          "end",
          "name",
          "depth",
          "strand",
          "thickStart",
          "thickEnd",
          "itemRgb"
        ]
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayMode": "collapsed"
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "ecoli_pggb"
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "showLabels": false
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_tier50",
      "name": "pggb graph bubbles (coarse tier, one node per bubble)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "ecoli_pggb.tier50"
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "ecoli_pggb_tier50-LinearBasicDisplay",
          "showLabels": false
        }
      ],
      "description": "The same graph as the segments track with one node per bubble instead of one per GFA segment, so a window far too wide for the fine index is still drawable: the whole 4.64 Mb pangenome is 1,088 nodes. Built from the graph's own vg deconstruct snarl VCF by scripts/snarls_to_bubble_bed.py plus scripts/build_bubble_tier.sh, keeping every bubble whose content is at least 50 bp so single-base alternatives fall into the backbone. Each node states what it collapsed: segments, traversals, and shortest and longest allele. Launch view -> Graph genome view (this region) opens it as a graph."
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_carriage",
      "name": "pggb graph: segment carriage (which strains carry each segment)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "ecoli_pggb"
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "ecoli_pggb_carriage-LinearBasicDisplay",
          "displayMode": "collapsed",
          "showLabels": false,
          "color": "jexl:feature.carriers==1?'#e31a1c':feature.carriers==2?'#fd8d3c':feature.carriers==3?'#feb24c':feature.carriers==4?'#fed976':feature.carriers==5?'#bdbdbd':'#eeeeee'",
          "legend": [
            { "label": "All 5 strains (core)", "color": "#bdbdbd" },
            { "label": "4 strains", "color": "#fed976" },
            { "label": "3 strains", "color": "#feb24c" },
            { "label": "2 strains", "color": "#fd8d3c" },
            { "label": "1 strain (private)", "color": "#e31a1c" }
          ]
        }
      ],
      "description": "The same segments as the track above, colored by how many haplotypes walk each one. build_pggb_tabix.sh records the carriers as an SM:Z: tag while it walks the graph's paths, so membership travels with the index. The depth track answers the same question as a smoothed count over windows; this answers it per segment, and clicking one lists the strains by name."
    },
    {
      "type": "SyntenyTrack",
      "trackId": "ecoli_cactus_ava",
      "name": "MC graph: all-vs-all synteny (halSynteny)",
      "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
      "adapter": {
        "type": "AllVsAllIndexedPAFAdapter",
        "pifGzLocation": {
          "uri": "ecoli_cactus_ava.pif.gz"
        },
        "index": {
          "location": {
            "uri": "ecoli_cactus_ava.pif.gz.tbi"
          }
        },
        "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "ecoli_cactus_variants",
      "name": "MC graph: pangenome variants (vs K12)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "ecoli_cactus.vcf.gz"
        },
        "index": {
          "location": {
            "uri": "ecoli_cactus.vcf.gz.tbi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantMatrixDisplay",
          "displayId": "ecoli_cactus_variants-matrix"
        }
      ]
    },
    {
      "type": "MafTrack",
      "trackId": "ecoli_cactus_maf",
      "name": "MC graph: whole-genome alignment (MAF, vs K12)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "MafTabixAdapter",
        "samples": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
        "uri": "ecoli_cactus.maf.bed.gz"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "ecoli_cactus_depth",
      "name": "MC graph: pangenome depth (paths over K12)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "ecoli_cactus_depth.bw"
        }
      }
    },
    {
      "type": "MultiQuantitativeTrack",
      "trackId": "ecoli_cactus_pav",
      "name": "MC graph: per-strain presence (odgi pav, vs K12)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "MultiWiggleAdapter",
        "subadapters": [
          {
            "type": "BigWigAdapter",
            "name": "Sakai",
            "bigWigLocation": {
              "uri": "ecoli_cactus_pav_Sakai.bw"
            }
          },
          {
            "type": "BigWigAdapter",
            "name": "CFT073",
            "bigWigLocation": {
              "uri": "ecoli_cactus_pav_CFT073.bw"
            }
          },
          {
            "type": "BigWigAdapter",
            "name": "NCTC86",
            "bigWigLocation": {
              "uri": "ecoli_cactus_pav_NCTC86.bw"
            }
          },
          {
            "type": "BigWigAdapter",
            "name": "IAI39",
            "bigWigLocation": {
              "uri": "ecoli_cactus_pav_IAI39.bw"
            }
          }
        ]
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_cactus_segments",
      "name": "MC graph: segments (whole graph, by locus)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "ecoli_cactus"
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "showLabels": false
        }
      ],
      "description": "The Minigraph-Cactus graph itself, indexed by locus the same way the pggb segments track is: build_pggb_tabix.sh walks the graph's P and W lines offline and writes the two tabix BEDs RgfaTabixAdapter reads. Launch view -> Graph genome view (this region) cuts the subgraph for whatever window is on screen, so the two builders' graphs can be opened over the same locus."
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "ecoli_e146_ont",
      "name": "E146 nanopore reads (vs K12)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "BamAdapter",
        "uri": "ecoli_e146_ont.bam"
      }
    }
  ],
  "plugins": [
    {
      "name": "GraphGenomeView",
      "esmUrl": "https://jbrowse.org/demos/graphgenomeviewer/jbrowse-plugin-graphgenomeviewer.esm.js"
    }
  ]
}