somatem-docs/workflow_mapping.json at main · treangenlab/somatem-docs · GitHub

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{
    "Pipeline 1": {
        "datatype": "16S",
        "analysis_type": "taxonomic-profiling",
        "sequencing_technology": "NanoPore or Pacbio",
        "workflow": "NanoPore or Pacbio -> NanoPlot -> chopper -> hostile -> NanoPlot -> Emu"
    },
    "Pipeline 2": {
        "datatype": "Isolate",
        "analysis_type": "assembly",
        "sequencing_technology": "NanoPore or Pacbio",
        "workflow": "NanoPore or Pacbio -> NanoPlot -> chopper -> hostile -> NanoPlot -> MetaFlye -> Minimap2 + Semibin2 -> CheckM2 -> Bakta"
    },
    "Pipeline 3": {
        "datatype": "Isolate",
        "analysis_type": "taxonomic-profiling",
        "sequencing_technology": "NanoPore or Pacbio",
        "workflow": "NanoPore or Pacbio -> NanoPlot -> chopper -> hostile -> NanoPlot -> Lemur + Magnet"
    },
    "Pipeline 4": {
        "datatype": "Metagenomics",
        "analysis_type": "genome-dynamics",
        "sequencing_technology": "NanoPore or Pacbio",
        "workflow": "NanoPore or Pacbio -> NanoPlot -> chopper -> hostile -> NanoPlot -> Rhea"
    },
    "Pipeline 5": {
        "datatype": "Metagenomics",
        "analysis_type": "assembly",
        "sequencing_technology": "NanoPore or Pacbio",
        "workflow": "NanoPore or Pacbio -> NanoPlot -> chopper -> hostile -> NanoPlot -> MetaFlye -> Minimap2 + Semibin2 -> CheckM2 -> Bakta"
    },
    "Pipeline 6": {
        "datatype": "Metagenomics",
        "analysis_type": "taxonomic-profiling",
        "sequencing_technology": "NanoPore or Pacbio",
        "workflow": "NanoPore or Pacbio -> NanoPlot -> chopper -> hostile -> NanoPlot -> Lemur + Magnet"
    },
    "Pipeline 7": {
        "datatype": "Metagenomics",
        "analysis_type": "pathogen",
        "sequencing_technology": "NanoPore or Pacbio",
        "workflow": "NanoPore or Pacbio -> NanoPlot -> chopper -> hostile -> NanoPlot -> Rhea"
    }
}