ArticleGigaScience2018
YAMP: a containerized workflow enabling reproducibility in metagenomics research.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes.Microbiology spectrum · 2022Pooled it
- Systemic and gut microbiome changes with metformin and liraglutide in youth-onset type 2 diabetes: the MIGHTY study.Gut microbes · 2025Trial
- Gut microbiome composition and function reflect socioeconomic deprivation.NPJ biofilms and microbiomes · 2026Article
- Short-chain fatty acids and their gut microbial pathways distinguish rheumatoid arthritis in discordant monozygotic twins.Annals of the rheumatic diseases · 2026Article
- Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.Nature communications · 2025Article
- Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.Journal of the American Society for Mass Spectrometry · 2025Article
- Red Cabbage Juice-Mediated Gut Microbiota Modulation Improves Intestinal Epithelial Homeostasis and Ameliorates Colitis.International journal of molecular sciences · 2023Article
- Unique trans-kingdom microbiome structural and functional signatures predict cognitive decline in older adults.GeroScience · 2023Article
- A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins.Scientific reports · 2023Article
- Physiologic colonic uptake ofEuropean journal of nuclear medicine and molecular imaging · 2021Article
- MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline.BMC bioinformatics · 2020Article
- Interplay between the human gut microbiome and host metabolism.Nature communications · 2019Article
- Conducting metagenomic studies in microbiology and clinical research.Applied microbiology and biotechnology · 2018Review
- Article
- Article
- Abnormalities in gut virome signatures linked with cognitive impairment in older adults.Gut microbesArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
YAMP ("Yet Another Metagenomics Pipeline") is a user-friendly workflow that enables the analysis of whole shotgun metagenomic data while using containerization to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system and offers seamless support for multiple job schedulers as well as for the Amazon AWS cloud. Although YAMP was developed to be ready to use by nonexperts, bioinformaticians will appreciate its flexibility, modularization, and simple customization.
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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.