ArticlemSystems2021
DOE JGI Metagenome Workflow.
Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed.
- Soil proteogenomics uncover microbial strategies for soil depth-specific carbon cycling under whole-soil warming conditions.Nature communications · 2026Article
- "Quadrupling" the protein family space with global metagenomics.Nucleic acids research · 2026Article
- Soil Acidification Enriches Antibiotic Resistome.Global change biology · 2026Article
- MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea.bioRxiv : the preprint server for biology · 2026Article
- Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.mSystems · 2026Article
- Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition.Nature communications · 2026Article
- Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem.Nature communications · 2026Article
- A comprehensive RNA virome from molluscan transcriptomes reveals extensive diversity and modular genome evolution.Virologica Sinica · 2026Article
- Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes.Scientific data · 2026Article
- Article
- Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes.The ISME journal · 2026Article
- Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.Nucleic acids research · 2026Article
- From microbial diversity to functional potential using dimensionality reduction.Frontiers in microbiology · 2026Article
- Arctic sea-ice ridges are biomass hotspots harboring diverse microbial communities.Communications earth & environment · 2026Article
- Dietary Macronutrient Intake and the Gut Microbiome in Adults Undergoing Bariatric Surgery for Obesity.medRxiv : the preprint server for health sciences · 2025Article
- Relating antimicrobial use to wastewater resistance gene patterns via metagenomic analysis of two neighboring treatment plants circa the COVID-19 pandemic.npj antimicrobials and resistance · 2025Article
- High-quality draft genome sequence ofMicrobiology resource announcements · 2025Article
- Suppression of gut colonization by multidrug-resistant Escherichia coli clinical isolates through cooperative niche exclusion.Nature communications · 2025Article
- Laboratory mice engrafted with natural gut microbiota possess a wildling-like phenotype.Nature communications · 2025Article
- Climate-driven succession in marine microbiome biodiversity and biogeochemical function.Nature communications · 2025Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic annotation; and binning of metagenomic data sets that are subsequently included into the Integrated Microbial Genomes and Microbiomes (IMG/M) (I.-M. A. Chen, K. Chu, K. Palaniappan, A. Ratner, et al., Nucleic Acids Res, 49:D751-D763, 2021, https://doi.org/10.1093/nar/gkaa939) comparative analysis system and provided for download via the JGI data portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here, we describe the different tools, databases, and parameters used at different steps of the workflow to help with the interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a workflow description language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi_meta_wdl). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in the Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, et al., Nucleic Acids Res, 49:D723-D733, 2021, https://doi.org/10.1093/nar/gkaa983).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.