{
  "title": "Real-time tracking of Lassa virus evolution",
  "maintainers": [
    { "name": "Jennifer Chang", "url": "https://bedford.io/team/jennifer-chang/" },
    { "name": "Richard Daodu", "url": "https://github.com/JoiRichi" },
    { "name": "Denise Kühnert", "url": "https://www.shh.mpg.de/person/54587/935000" },
    { "name": "the Nextstrain team", "url": "https://nextstrain.org/team" }
  ],
  "data_provenance": [
    {
      "name": "GenBank",
      "url": "https://www.ncbi.nlm.nih.gov/genbank/"
    }
  ],
  "build_url": "https://github.com/nextstrain/lassa",
  "colorings": [
    {
      "key": "gt",
      "title": "Genotype",
      "type": "categorical"
    },
    {
      "key": "num_date",
      "title": "Date",
      "type": "continuous"
    },
    {
      "key": "country",
      "title": "Country",
      "type": "categorical"
    },
    {
      "key": "division",
      "title": "Admin Division",
      "type": "categorical"
    },
    {
      "key": "host",
      "title": "Host",
      "type": "categorical"
    },
    {
      "key": "abbr_authors",
      "title": "Authors",
      "type": "categorical"
    },
    {
      "key": "clade_membership",
      "title": "Clade",
      "type": "categorical"
    },
    {
      "key": "lineage_name",
      "title": "Lineage name",
      "type": "categorical"
    },
    { "key": "reference",
      "title": "Reference",
      "type": "categorical"
    }
  ],
  "geo_resolutions": [
    "country"
  ],
  "display_defaults": {
    "map_triplicate": false,
    "color_by": "clade_membership",
    "distance_measure": "div"
  },
  "filters": [
    "country",
    "division",
    "host",
    "abbr_authors",
    "clade_membership",
    "lineage_name"
  ],
  "extensions": {
    "clade_node_attrs": [
        {
          "name": "lineage_name",
          "displayName": "Lassa lineage name",
          "description": "Global lassa lineages based on [citation here]."
        }
      ],
    "nextclade": {
      "pathogen": {
        "schemaVersion":"3.0.0",
        "defaultCds": "GPC",
        "attributes": {
          "name": "Lassa Global Tree",
          "reference name": "Josiah",
          "reference accession": "NC_004296"
        },
        "alignmentParams": {
          "penaltyGapExtend": 1,
          "penaltyGapOpen": 8,
          "penaltyGapOpenInFrame": 9,
          "penaltyGapOpenOutOfFrame": 10,
          "penaltyMismatch": 1,
          "scoreMatch": 5,
          "retryReverseComplement": true,
          "allowedMismatches": 10,
          "minSeedCover": 0.01,
          "minLength": 800
        },
        "qc": {
          "missingData": {
            "enabled": true,
            "missingDataThreshold": 20,
            "scoreBias": 4
          },
          "mixedSites": {
            "enabled": true,
            "mixedSitesThreshold": 4
          },
          "frameShifts": {
            "enabled": true
          },
          "stopCodons": {
            "enabled": true
          },
          "privateMutations": {
            "enabled": true,
            "cutoff": 12,
            "typical": 4,
            "weightLabeledSubstitutions": 1,
            "weightReversionSubstitutions": 1,
            "weightUnlabeledSubstitutions": 1
          },
          "snpClusters": {
            "enabled": true,
            "clusterCutOff": 3,
            "scoreWeight": 50,
            "windowSize": 50
          }
        }
      }
    }
  }
}
