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README.md

GeneLab bioinformatics processing pipeline for Illumina amplicon sequencing data

The document GL-DPPD-7104-B.md holds an overview and example commands for how GeneLab processes Illumina amplicon sequencing datasets. See the Repository Links descriptions below for more information. Processed data output files and processing code are provided for each GLDS dataset in the Open Science Data Repository (OSDR).

Note: The exact processing commands and AmpIllumina version used for specific GLDS datasets can be found in the *_processing_info.zip file under "Files" for each respective GLDS dataset in the Open Science Data Repository (OSDR).

Repository Links

  • Pipeline_GL-DPPD-7104_Versions

    • Contains documentation for current and previous versions of the GeneLab Illumina Amplicon Sequencing Data Processing Pipeline (AmpIllumina)

  • Workflow_Documentation

    • Contains instructions for installing and running the GeneLab AmpIllumina workflow

  • GLDS_Processing_Scripts

    • Contains the exact processing commands and AmpIllumina version used for select GLDS datasets that have been released and are available in the Open Science Data Repository (OSDR)

      Note: Exact processing commands and AmpIllumina version used for datasets not available in this sub-directory can be found in the *_processing_info.zip file under "Files" for each respective GLDS dataset in the Open Science Data Repository (OSDR).

Developed by:
Michael D. Lee ([email protected])
Maintained by:
Michael D. Lee ([email protected])
Alexis Torres ([email protected])
Amanda Saravia-Butler ([email protected])