ArticleGigaScience2019
MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Bioinformatic tools for microbiome analysis: from raw sequences to biological insights.Frontiers in microbiology · 2026Review
- Diversity of antibiotic resistance genes and mobile genetic elements of Sof Umer Cave microbiomes, Ethiopia.BMC genomic data · 2025Article
- Differences in Microbial Community Structure Determine the Functional Specialization of Gut Segments ofMicroorganisms · 2025Article
- Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization.Microbiome · 2024Article
- On the limits of 16S rRNA gene-based metagenome prediction and functional profiling.Microbial genomics · 2024Article
- Analysis and Interpretation of metagenomics data: an approach.Biological procedures online · 2022Review
- Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome.Nature communications · 2021Article
- Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.Microbial genomics · 2020Review
- Article
- Article
- Integrating Computational Methods to Investigate the Macroecology of Microbiomes.Frontiers in genetics · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
backgroundCurrent methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to a generic database of proteins or reference microbial genomes.
resultsWe developed MGS-Fast, an analysis approach for shotgun whole-genome metagenomic data utilizing Bowtie2 DNA-DNA alignment of reads that is an alternative to using the integrated catalog of reference genes database of well-annotated genes compiled from human microbiome data. This method is rapid and provides high-stringency matches (>90% DNA sequence identity) of the metagenomics reads to genes with annotated functions. We demonstrate the use of this method with data from a study of liver disease and synthetic reads, and Human Microbiome Project shotgun data, to detect differentially abundant Kyoto Encyclopedia of Genes and Genomes gene functions in these experiments. This rapid annotation method is freely available as a Galaxy workflow within a Docker image.
conclusionsMGS-Fast can confidently transfer functional annotations from gene databases to metagenomic reads, with speed and accuracy.
Indexed as
Identifiers
What OpenQuestion holds
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.