jbrowse2-plugin-nuccontent

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"
      }
    ]
  }
]

Bug Reports/Issues/Contributions

Bug reports and issues for this plugin can be submitted via this Github repository:

• https://github.com/jjrozewicki/jbrowse2-plugin-nuccontent

Pull requests that include documentation of improvements/fixes will be considered, but may not be immediately accepted.

Development

Dependencies for this project can be downloaded through yarn:

• npx yarn

This project can be built with the command:

• npx yarn build