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@microbiomedata

National Microbiome Data Collaborative

National Microbiome Data Collaborative

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  1. nmdc-schema nmdc-schema Public

    National Microbiome Data Collaborative (NMDC) unified data model

    Python 44 9

  2. docs docs Public

    User-facing, web-based documentation about the NMDC

    Dockerfile 2 3

Repositories

Showing 10 of 80 repositories
  • nmdc-runtime Public

    Runtime system for NMDC data management and orchestration

    microbiomedata/nmdc-runtime’s past year of commit activity
    Python 7 6 126 (3 issues need help) 8 Updated Dec 15, 2025
  • nmdc-server Public

    Data portal client and server for NMDC.

    microbiomedata/nmdc-server’s past year of commit activity
    Python 12 0 121 22 Updated Dec 15, 2025
  • ReadbasedAnalysis Public

    The pipeline takes in sequencing files (single- or paired-end) and profiles them using multiple taxonomic classification tools

    microbiomedata/ReadbasedAnalysis’s past year of commit activity
    HTML 2 6 0 0 Updated Dec 12, 2025
  • nmdc-aggregator Public

    Scripts that periodically aggregate data related to KEGG search

    microbiomedata/nmdc-aggregator’s past year of commit activity
    Python 0 0 4 1 Updated Dec 11, 2025
  • nmdc_automation Public

    Prototype automation

    microbiomedata/nmdc_automation’s past year of commit activity
    Python 2 2 66 10 Updated Dec 11, 2025
  • nmdc_api_utilities Public

    A library designed to simplify various research tasks for users looking to leverage the NMDC (National Microbiome Data Collaborative) APIs. The library provides a collection of general-purpose functions that facilitate easy access, manipulation, and analysis of microbiome data.

    microbiomedata/nmdc_api_utilities’s past year of commit activity
    Python 4 0 4 2 Updated Dec 11, 2025
  • metadata-for-user-facility-template-transformations Public

    CLI tool to convert metadata submissions from the NMDC submission portal to user facility Excel templates

    microbiomedata/metadata-for-user-facility-template-transformations’s past year of commit activity
    Python 0 0 14 (1 issue needs help) 2 Updated Dec 10, 2025
  • metaMAGs Public

    Workflow for metagenome assembled genomes generation.

    microbiomedata/metaMAGs’s past year of commit activity
    Python 8 4 1 1 Updated Dec 10, 2025
  • nmdc_mass_spectrometry_metadata_generation Public

    Mass spectrometry metadata generation

    microbiomedata/nmdc_mass_spectrometry_metadata_generation’s past year of commit activity
    Python 2 0 6 2 Updated Dec 10, 2025
  • metaT_ReadsQC Public

    Workflow for metatranscriptome quality control

    microbiomedata/metaT_ReadsQC’s past year of commit activity
    WDL 0 0 0 0 Updated Dec 10, 2025
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