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Related Experiment Video

Updated: Nov 5, 2025

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

37.5K

DOE JGI Metagenome Workflow.

Alicia Clum1, Marcel Huntemann2, Brian Bushnell2

  • 1Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA aclum@lbl.gov.

Msystems
|May 19, 2021
PubMed
Summary

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This summary is machine-generated.

The DOE JGI Metagenome Workflow processes metagenomic data, enabling comprehensive analysis of microbial communities. This workflow standardizes data processing for thousands of samples, facilitating discovery of novel taxa and functional insights.

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Metagenomic data analysis requires robust, scalable workflows for processing diverse microbial communities.
  • The DOE Joint Genome Institute (JGI) developed a standardized workflow to address these challenges.

Purpose of the Study:

  • To describe the DOE JGI Metagenome Workflow, detailing its tools, databases, and parameters.
  • To enable researchers to utilize this workflow for their own metagenomic data analysis.
  • To illustrate workflow capabilities using publicly available sediment metagenomes.

Main Methods:

  • The workflow integrates read filtering, error correction, assembly, structural and functional annotation, and binning.
  • It utilizes specific tools, databases, and parameters, with modules available via WDL and a web service.
Keywords:
IMGJGISOPannotationassemblybinningmetagenomics

Related Experiment Videos

Last Updated: Nov 5, 2025

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

37.5K
  • Demonstration involves processing 20 sediment metagenomes to assess computational requirements and results.

    • Main Results:

    • The workflow processes thousands of metagenome samples annually, handling variations in community complexity and sequencing depth.
    • Results are provided in standard formats (e.g., fasta, gff) for integration into the IMG/M system.
    • As of July 2020, 7,155 JGI metagenomes have been processed, demonstrating workflow scalability and utility.

    Conclusions:

    • The DOE JGI Metagenome Workflow provides a standardized and optimized pipeline for comprehensive metagenomic data analysis.
    • It supports downstream applications from community composition assessment to genome-resolved metagenomics and novel taxa discovery.
    • The workflow is crucial for consistent analysis of large-scale metagenomic datasets.