Prepare "proksee assemble" Outputs for Display in Proksee Viewer

[emarinier]

We should first come up with an idea for what data will be displayed and what form it will have. Then, we should run that idea by Jason to make sure that it will work with the viewer.

When in agreement about content and form, have the data written in the agreed form to a specific output location.

[emarinier]

JSON Format Report

Example:

{
  "sequencingTechnology": "Illumina",
  "speciesName": "Listeria monocytogenes",

  "assemblyQuality”: [
    {
      "n50": 150000,
      "l50": 30,
      "numContigs": 60,
      "assemblySize": 3100000,
    }
  ],

  "readQuality": [
    {
      (read quality attributes)
    }
  ],

  "heuristic_evaluation": [
    {
      "n50": "pass",
      "n50Report": "The N50 looks normal.",
      "l50": "pass",
      "l50Report": "The L50 looks normal.",
      "numContigs": "warn",
      "numContigsReport": "The number of contigs is less than expected.",
      "assemblySize": "fail",
      "assemblySizeReport": The assembly size is larger than expected."
    }
  ],

  "ml_evaluation": [
    {
      "probability": 0.61,
      "report": "The assembly appears similar to RefSeq assemblies."
    }
  ]
}

[emarinier]

@sciguy

Do you have any thoughts on using a format like this? Does it seem reasonable to go ahead with implementing something like this?

[sciguy]

@emarinier This format looks good to me.