spec_version: 0.1.0
repository: waldronlab/agent-protocols
generated_at: '2026-09-14T03:35:49Z'
protocols:
- name: humann4-augmented-clustering
  description: Predict ORFs and perform augmented UniRef-compatible protein clustering.
  version: 1.0.0
  authors:
  - name: Levi Waldron
    orcid: 0000-0003-2725-0694
  reviews:
  - name: Curtis Huttenhower
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  - name: Eric Franzosa
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  date: '2026-08-08'
  status: stable
  license: CC-BY-4.0
  type: atomic
  artifact_doi: null
  collection_doi: 10.5281/zenodo.22731694
  protocol_citation: 10.7554/eLife.65088
  method_origin_citation: 10.1016/j.cell.2019.01.001
  upstream_repositories:
  - https://github.com/biobakery/humann
  - https://github.com/biobakery/metaphlan
  - https://github.com/biobakery/biobakery-nextflow
  database_urls:
  - http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/
  - ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/
  protocols_used: []
  key_packages: []
  category: metagenomics
  tags:
  - humann
  - chocophlan
  - database
  - uniref
  - clustering
  - mmseqs2
  - diamond
  protocol_url: https://raw.githubusercontent.com/waldronlab/agent-protocols/main/protocols/humann4-augmented-clustering/protocol.md
- name: humann4-chocophlan-build
  description: Construct the HUMAnN 4 ChocoPhlAn nucleotide pangenome database.
  version: 1.0.0
  authors:
  - name: Levi Waldron
    orcid: 0000-0003-2725-0694
  reviews:
  - name: Curtis Huttenhower
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  - name: Eric Franzosa
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  date: '2026-08-08'
  status: stable
  license: CC-BY-4.0
  type: atomic
  artifact_doi: null
  collection_doi: 10.5281/zenodo.22731694
  protocol_citation: 10.7554/eLife.65088
  upstream_repositories:
  - https://github.com/biobakery/humann
  - https://github.com/biobakery/metaphlan
  - https://github.com/biobakery/biobakery-nextflow
  database_urls:
  - http://huttenhower.sph.harvard.edu/humann_data/chocophlan/
  - http://cmprod1.cibio.unitn.it/databases/chocophlan/
  protocols_used: []
  key_packages: []
  category: metagenomics
  tags:
  - humann
  - chocophlan
  - database
  - pangenome
  - bowtie2
  protocol_url: https://raw.githubusercontent.com/waldronlab/agent-protocols/main/protocols/humann4-chocophlan-build/protocol.md
- name: humann4-database-build
  description: End-to-end composite pipeline for constructing HUMAnN 4 reference databases
    from MetaPhlAn 4.2 SGBs.
  version: 1.0.0
  authors:
  - name: Levi Waldron
    orcid: 0000-0003-2725-0694
  reviews:
  - name: Curtis Huttenhower
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  - name: Eric Franzosa
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  date: '2026-08-18'
  status: stable
  license: CC-BY-4.0
  type: composite
  artifact_doi: null
  collection_doi: 10.5281/zenodo.22731694
  protocol_citation: 10.7554/eLife.65088
  upstream_repositories:
  - https://github.com/biobakery/humann
  - https://github.com/biobakery/metaphlan
  - https://github.com/biobakery/biobakery-nextflow
  database_urls:
  - http://huttenhower.sph.harvard.edu/humann_data/chocophlan/
  - http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/
  - http://huttenhower.sph.harvard.edu/humann_data/mapping/
  protocols_used:
  - name: humann4-sgb-aggregation
    repository: waldronlab/agent-protocols
    version: 1.0.0
  - name: humann4-augmented-clustering
    repository: waldronlab/agent-protocols
    version: 1.0.0
  - name: humann4-chocophlan-build
    repository: waldronlab/agent-protocols
    version: 1.0.0
  - name: humann4-translated-search-build
    repository: waldronlab/agent-protocols
    version: 1.0.0
  - name: humann4-utility-mapping
    repository: waldronlab/agent-protocols
    version: 1.0.0
  key_packages: []
  category: metagenomics
  tags:
  - humann
  - chocophlan
  - database
  - pipeline
  - composite
  protocol_url: https://raw.githubusercontent.com/waldronlab/agent-protocols/main/protocols/humann4-database-build/protocol.md
- name: humann4-sgb-aggregation
  description: Aggregate and subsample isolate genomes and MAGs for MetaPhlAn 4.2
    SGBs.
  version: 1.0.0
  authors:
  - name: Levi Waldron
    orcid: 0000-0003-2725-0694
  reviews:
  - name: Curtis Huttenhower
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  - name: Eric Franzosa
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  date: '2026-08-08'
  status: stable
  license: CC-BY-4.0
  type: atomic
  artifact_doi: null
  collection_doi: 10.5281/zenodo.22731694
  protocol_citation: 10.7554/eLife.65088
  method_origin_citation: 10.1016/j.cell.2019.01.001
  upstream_repositories:
  - https://github.com/biobakery/metaphlan
  - https://github.com/biobakery/panphlan
  - https://github.com/biobakery/biobakery-nextflow
  database_urls:
  - http://cmprod1.cibio.unitn.it/databases/MetaPhlAn/
  - http://cmprod1.cibio.unitn.it/databases/PanPhlAn/
  protocols_used: []
  key_packages: []
  category: metagenomics
  tags:
  - humann
  - chocophlan
  - database
  - sgb
  - metaphlan
  protocol_url: https://raw.githubusercontent.com/waldronlab/agent-protocols/main/protocols/humann4-sgb-aggregation/protocol.md
- name: humann4-translated-search-build
  description: Compile the HUMAnN 4 translated search database.
  version: 1.0.0
  authors:
  - name: Levi Waldron
    orcid: 0000-0003-2725-0694
  reviews:
  - name: Curtis Huttenhower
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  - name: Eric Franzosa
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  date: '2026-08-08'
  status: stable
  license: CC-BY-4.0
  type: atomic
  artifact_doi: null
  collection_doi: 10.5281/zenodo.22731694
  protocol_citation: 10.7554/eLife.65088
  upstream_repositories:
  - https://github.com/biobakery/humann
  - https://github.com/biobakery/biobakery-nextflow
  database_urls:
  - http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/
  protocols_used: []
  key_packages: []
  category: metagenomics
  tags:
  - humann
  - database
  - translated-search
  - diamond
  - uniref
  protocol_url: https://raw.githubusercontent.com/waldronlab/agent-protocols/main/protocols/humann4-translated-search-build/protocol.md
- name: humann4-utility-mapping
  description: Generate HUMAnN 4 utility mapping databases for functional annotation.
  version: 1.0.0
  authors:
  - name: Levi Waldron
    orcid: 0000-0003-2725-0694
  reviews:
  - name: Curtis Huttenhower
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  - name: Eric Franzosa
    date: '2026-08-18'
    protocol_version: 1.0.0
    status: approved
  date: '2026-08-08'
  status: stable
  license: CC-BY-4.0
  type: atomic
  artifact_doi: null
  collection_doi: 10.5281/zenodo.22731694
  protocol_citation: 10.7554/eLife.65088
  upstream_repositories:
  - https://github.com/biobakery/humann
  - https://github.com/eggnogdb/eggnog-mapper
  - https://github.com/biobakery/biobakery-nextflow
  database_urls:
  - http://huttenhower.sph.harvard.edu/humann_data/mapping/
  - http://huttenhower.sph.harvard.edu/humann_data/legacy_dbs/
  protocols_used: []
  key_packages: []
  category: metagenomics
  tags:
  - humann
  - database
  - functional-annotation
  - eggnog-mapper
  - uniprot
  protocol_url: https://raw.githubusercontent.com/waldronlab/agent-protocols/main/protocols/humann4-utility-mapping/protocol.md
- name: independent-filtering-variance
  description: Filter high-throughput features by overall variance or mean across
    all samples before a separately specified downstream analysis.
  version: 1.2.1
  authors:
  - name: Otto Infield-Harm
  - name: Levi Waldron
    orcid: 0000-0003-2725-0694
  reviews:
  - name: Levi Waldron
    orcid: 0000-0003-2725-0694
    date: '2026-09-10'
    protocol_version: 1.2.1
    status: approved
  date: '2026-09-03'
  status: stable
  type: atomic
  artifact_doi: null
  collection_doi: 10.5281/zenodo.22731694
  protocol_citation: 10.1073/pnas.0914005107
  license: CC-BY-4.0
  method_origin_citation: 10.1073/pnas.0914005107
  protocols_used: []
  category: Statistical Analysis
  tags:
  - filtering
  - variance
  - mean
  - high-throughput
  protocol_url: https://raw.githubusercontent.com/waldronlab/agent-protocols/main/protocols/independent-filtering-variance/protocol.md