{
  "id": "lib-process:bioinformatics--shotgun-metagenomics",
  "_kind": "LibraryProcess",
  "_file": "generated-library/processes.yaml",
  "_cluster": "generated-library",
  "attributes": {
    "displayName": "shotgun-metagenomics",
    "description": "Shotgun Metagenomics Pipeline - Comprehensive analysis of shotgun metagenomic sequencing\ndata for taxonomic and functional profiling of microbial communities with strain-level resolution.",
    "libraryPath": "library/specializations/domains/science/bioinformatics/shotgun-metagenomics.js",
    "specialization": "bioinformatics",
    "references": [
      "- MetaPhlAn4: https://github.com/biobakery/MetaPhlAn\n- HUMAnN3: https://huttenhower.sph.harvard.edu/humann/\n- Kraken2: https://ccb.jhu.edu/software/kraken2/\n- MEGAHIT: https://github.com/voutcn/megahit\n- CARD Database: https://card.mcmaster.ca/"
    ],
    "example": "const result = await orchestrate('specializations/domains/science/bioinformatics/shotgun-metagenomics', {\n  projectName: 'Environmental Microbiome Study',\n  samples: [{ id: 'sample1', r1: '/data/sample1_R1.fq.gz', r2: '/data/sample1_R2.fq.gz' }],\n  metadata: { environment: ['soil', 'water'] },\n  hostGenome: 'GRCh38'\n});",
    "usesAgents": [
      "general-purpose"
    ]
  },
  "outgoingEdges": [
    {
      "from": "lib-process:bioinformatics--shotgun-metagenomics",
      "to": "skill-area:data-analysis",
      "kind": "lib_requires_skill_area",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--shotgun-metagenomics",
      "to": "skill-area:statistical-analysis",
      "kind": "lib_requires_skill_area",
      "attributes": {
        "weight": 0.7
      }
    },
    {
      "from": "lib-process:bioinformatics--shotgun-metagenomics",
      "to": "skill-area:python-data-pipelines",
      "kind": "lib_requires_skill_area",
      "attributes": {
        "weight": 0.5
      }
    },
    {
      "from": "lib-process:bioinformatics--shotgun-metagenomics",
      "to": "domain:bioinformatics",
      "kind": "lib_applies_to_domain",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--shotgun-metagenomics",
      "to": "role:research-engineer",
      "kind": "lib_involves_role",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--shotgun-metagenomics",
      "to": "role:biomedical-engineer",
      "kind": "lib_involves_role",
      "attributes": {
        "weight": 0.7
      }
    },
    {
      "from": "lib-process:bioinformatics--shotgun-metagenomics",
      "to": "workflow:experiment-design",
      "kind": "lib_implements_workflow",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--shotgun-metagenomics",
      "to": "specialization:biomedical-informatics",
      "kind": "lib_belongs_to_specialization",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--shotgun-metagenomics",
      "to": "specialization:bioinformatics",
      "kind": "lib_belongs_to_specialization",
      "attributes": {
        "weight": 0.9
      }
    }
  ],
  "incomingEdges": []
}