ArticleBriefings in bioinformatics2019
MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis.
Article in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
59 citing papers in PubMed.
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- Marine Community Metabolomes in the Eastern Tropical North Pacific Oxygen Deficient Zone Reveal Glycine Betaine as a Metabolic Link Between Prochlorococcus and SAR11.Environmental microbiology · 2025Article
- Characterization of antibiotic resistance genes in soils from agroecosystems of the Brazilian Amazon.Frontiers in microbiology · 2025Article
- FoodMicroDB: A microbiome database for composition and time-series research in food.iMetaOmics · 2024Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics.Nucleic acids research · 2024Article
- Review
- Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome.Microbiome · 2024Article
- Pre-Bleaching Coral Microbiome Is Enriched in Beneficial Taxa and Functions.Microorganisms · 2024Article
- Study of the Microbiome of the Cretan Sour Cream Staka Using Amplicon Sequencing and Shotgun Metagenomics and Isolation of Novel Strains with an Important Antimicrobial Potential.Foods (Basel, Switzerland) · 2024Article
- A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data.Biochemical genetics · 2024Review
- The Human Gut and Dietary Salt: TheNutrients · 2024Article
- NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes.Nucleic acids research · 2024Article
- Article
- Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater.BMC microbiology · 2023Article
- Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale.Microbial ecology · 2023Article
- Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections withFrontiers in cellular and infection microbiology · 2023Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
As technologies change, MG-RAST is adapting. Newly available software is being included to improve accuracy and performance. As a computational service constantly running large volume scientific workflows, MG-RAST is the right location to perform benchmarking and implement algorithmic or platform improvements, in many cases involving trade-offs between specificity, sensitivity and run-time cost. The work in [Glass EM, Dribinsky Y, Yilmaz P, et al. ISME J 2014;8:1-3] is an example; we use existing well-studied data sets as gold standards representing different environments and different technologies to evaluate any changes to the pipeline. Currently, we use well-understood data sets in MG-RAST as platform for benchmarking. The use of artificial data sets for pipeline performance optimization has not added value, as these data sets are not presenting the same challenges as real-world data sets. In addition, the MG-RAST team welcomes suggestions for improvements of the workflow. We are currently working on versions 4.02 and 4.1, both of which contain significant input from the community and our partners that will enable double barcoding, stronger inferences supported by longer-read technologies, and will increase throughput while maintaining sensitivity by using Diamond and SortMeRNA. On the technical platform side, the MG-RAST team intends to support the Common Workflow Language as a standard to specify bioinformatics workflows, both to facilitate development and efficient high-performance implementation of the community's data analysis tasks.
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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.