Standardized Bioinformatics Workflows

The NMDC supported standardized workflows for processing microbiome omics data

Access through DockerHub

Containerized software to run multi-omics workflows.

Access through GitHub

Workflow code available in Workflow Description Language (WDL).

Microbiome datasets are often processed with different tools and pipelines, which presents challenges for reuse and cross-study comparisons. To address these challenges, the NMDC integrated production quality, open-source bioinformatics tools into accessible standardized workflows for processing omics data (e.g., metagenome, metatranscriptome, metaproteome, and metabolome data) to produce interoperable and reusable annotated data products. These workflows further the NMDC’s commitment to the FAIR data principles.

The NMDC workflows included bioinformatics tools developed by the Joint Genome Institute (JGI) and Environmental Molecular Sciences Laboratory (EMSL), among others. The workflows developed and used in production at JGI and EMSL are used to process thousands of datasets annually and have been extensively benchmarked to ensure the generation of high-quality data.

The NMDC workflows are publicly available through GitHub and DockerHub as standalone, containerized workflows, offering a unique opportunity for any institute or individual to obtain, install, and run the workflows in their own environments.

Metagenome workflow

The NMDC metagenome pipeline includes reads QC, read-based taxonomy classification, metagenome assembly, metagenome annotation, and metagenome assembled genomes (MAGs) workflows

Metatranscriptome workflow

Takes in raw metatranscriptome data, filters reads for quality, removes rRNA reads, then assembles and annotates transcripts

The NMDC Standardized Bioinformatics Workflows

To date, the standardized production-quality workflows developed by the JGI and EMSL have largely been limited to the facilities for which they were developed. We provide access to these standardized workflows to process multi-omics data and produce interoperable annotated data.

Metabolome workflow

The GC-MS based workflow performs signal noise reduction, m/z based Chromatogram Peak Deconvolution, abundance threshold calculation, peak picking, spectral similarity calculation and molecular search, similarity score calculation, and confidence filtering

Documentation

The NMDC documentation provides additional information on each workflow, their standardized parameters, any associated databases, versions, and the tools associated with each workflow.