Jbrowse2-plugin-nuccontent NPM

jbrowse2-plugin-nuccontent

This NucContent plugin for JBrowse2 is designed to allow easy calculation of statistics like GC content, but is also customizable enough for calculating other kinds of statistics (e.g. soft-masked nucleotides).

Install

For use in `@jbrowse/react-linear-view`

yarn add jbrowse2-plugin-nuccontent

For use in JBrowse Web

Add the appropriate plugin and track settings based on the example below.

"plugins": [
  {
    "name": "NucContent",
    "url": "https://unpkg.com/jbrowse2-plugin-nuccontent/dist/jbrowsepluginnuccontent.umd.production.min.js"
  }
}

Example Track Config

This plugin takes a standard Sequence Adapter configuration to load the sequence data that will be used for statistics. This could be the sequence files used for the main assembly, but could also be other kinds of sequence data that are mapped to the main assembly.

"tracks": [
  {
    "name": "GC Content (Dynamic)",
    "trackId": "gc_content_dynamic",
    "type": "NucContentTrack",
    "assemblyNames": [
      "SL4.0"
    ],
    "adapter": {
      "type": "NucContentAdapter",
      "sequenceAdapter": {
        "type": "BgzipFastaAdapter",
        "faiLocation": {
          "uri": "./sample_config/S_lycopersicum_chromosomes.4.00.fa.gz.fai"
        },
        "fastaLocation": {
          "uri": "./sample_config/S_lycopersicum_chromosomes.4.00.fa.gz"
        },
        "gziLocation": {
          "uri": "./sample_config/S_lycopersicum_chromosomes.4.00.fa.gz.gzi"
        }
      },
      "charactersA": "Gg",
      "charactersB": "Cc",
      "charactersAll": "AaTtGgCc",
      "windowSize": 10000,
      "windowOverlap": 0
    },
    "displays": [
      {
        "displayId": "gc_content_dynamic-NucContentDisplay",
        "maxScore": 0.7,
        "minScore": 0.3,
        "renderers": {
          "DensityRenderer": {
            "type": "DensityRenderer"
          },
          "LinePlotRenderer": {
            "type": "LinePlotRenderer"
          },
          "XYPlotRenderer": {
            "type": "XYPlotRenderer"
          }
        },
        "type": "NucContentDisplay"
      }
    ]
  }
]