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YAMP: a containerised workflow enabling reproducibility in metagenomics research
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity
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Integrative Personal Omics Profiles during Periods of Weight Gain and Loss
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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities
inferredcites →https://doi.org/10.1038/533452aopenalex-snapshot
1,500 scientists lift the lid on reproducibility
inferredcites →https://doi.org/10.1038/ismej.2009.72openalex-snapshot
Systematic artifacts in metagenomes from complex microbial communities
inferredcites →https://doi.org/10.1038/nature11209openalex-snapshot
A framework for human microbiome research
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nbt.3820openalex-snapshot
Nextflow enables reproducible computational workflows
inferredcites →https://doi.org/10.1038/nbt.3935openalex-snapshot
Shotgun metagenomics, from sampling to analysis
inferredcites →https://doi.org/10.1038/ng.295openalex-snapshot
Repeatability of published microarray gene expression analyses
inferredcites →https://doi.org/10.1038/nmeth.3589openalex-snapshot
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
inferredcites →https://doi.org/10.1038/nmeth.4458openalex-snapshot
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/npre.2011.5886openalex-snapshot
CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0
inferredcites →https://doi.org/10.1038/s41564-017-0075-5openalex-snapshot
Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice
inferredcites →https://doi.org/10.1038/srep06957openalex-snapshot
Assessment of quality control approaches for metagenomic data analysis
inferredcites →https://doi.org/10.1073/pnas.0809964106openalex-snapshot
Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame
inferredcites →https://doi.org/10.1073/pnas.1519288112openalex-snapshot
Library preparation methodology can influence genomic and functional predictions in human microbiome research
inferredcites →https://doi.org/10.1093/bib/bbw020openalex-snapshot
A review of bioinformatic pipeline frameworks
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btl117openalex-snapshot
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
inferredcites →https://doi.org/10.1093/bioinformatics/btw183openalex-snapshot
MOCAT2: a metagenomic assembly, annotation and profiling framework
inferredcites →https://doi.org/10.1093/bioinformatics/btx709openalex-snapshot
Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations
inferredcites →https://doi.org/10.1093/gigascience/gix048openalex-snapshot
Bio-Docklets: virtualization containers for single-step execution of NGS pipelines
inferredcites →https://doi.org/10.1093/nar/gki866openalex-snapshot
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
inferredcites →https://doi.org/10.1093/nar/gkt919openalex-snapshot
IMG/M 4 version of the integrated metagenome comparative analysis system
inferredcites →https://doi.org/10.1093/nar/gkv1164openalex-snapshot
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
inferredcites →https://doi.org/10.1093/nar/gkw343openalex-snapshot
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
inferredcites →https://doi.org/10.1093/nar/gkx967openalex-snapshot
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
inferredcites →https://doi.org/10.1101/gr.094508.109openalex-snapshot
Windshield splatter analysis with the Galaxy metagenomic pipeline
inferredcites →https://doi.org/10.1101/gr.184879.114openalex-snapshot
Using populations of human and microbial genomes for organism detection in metagenomes
inferredcites →https://doi.org/10.1111/j.1654-1103.2003.tb02228.xopenalex-snapshot
VEGAN, a package of R functions for community ecology
inferredcites →https://doi.org/10.1126/science.1213847openalex-snapshot
Reproducible Research in Computational Science
inferredcites →https://doi.org/10.1126/scitranslmed.3008599openalex-snapshot
The Placenta Harbors a Unique Microbiome
inferredcites →https://doi.org/10.1145/1376616.1376772openalex-snapshot
Provenance and scientific workflows
inferredcites →https://doi.org/10.1145/2723872.2723882openalex-snapshot
An introduction to Docker for reproducible research
inferredcites →https://doi.org/10.1186/1471-2105-10-359openalex-snapshot
Analysis and comparison of very large metagenomes with fast clustering and functional annotation
inferredcites →https://doi.org/10.1186/1471-2105-11-187openalex-snapshot
Artificial and natural duplicates in pyrosequencing reads of metagenomic data
inferredcites →https://doi.org/10.1186/1471-2105-12-356openalex-snapshot
CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing
inferredcites →https://doi.org/10.1186/1471-2105-9-386openalex-snapshot
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
inferredcites →https://doi.org/10.1186/gb-2013-14-1-r2openalex-snapshot
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
inferredcites →https://doi.org/10.1186/s12859-017-1770-1openalex-snapshot
CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction
inferredcites →https://doi.org/10.1186/s12864-016-3063-xopenalex-snapshot
Computational workflow for the fine-grained analysis of metagenomic samples
inferredcites →https://doi.org/10.1186/s12864-018-5094-yopenalex-snapshot
Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
inferredcites →https://doi.org/10.1186/s13059-015-0759-1openalex-snapshot
Host genetic variation impacts microbiome composition across human body sites
inferredcites →https://doi.org/10.1186/s13059-016-1116-8openalex-snapshot
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
inferredcites →https://doi.org/10.1186/s13062-015-0071-8openalex-snapshot
Experiences with workflows for automating data-intensive bioinformatics
inferredcites →https://doi.org/10.1186/s13742-016-0135-4openalex-snapshot
Tools and techniques for computational reproducibility
inferredcites →https://doi.org/10.1371/journal.pbio.1002165openalex-snapshot
The Economics of Reproducibility in Preclinical Research
inferredcites →https://doi.org/10.1371/journal.pcbi.1002358openalex-snapshot
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
inferredcites →https://doi.org/10.1371/journal.pone.0017288openalex-snapshot
Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
inferredcites →https://doi.org/10.1371/journal.pone.0038234openalex-snapshot
The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements
inferredcites →https://doi.org/10.1371/journal.pone.0052249openalex-snapshot
FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads
inferredcites →https://doi.org/10.1371/journal.pone.0080278openalex-snapshot
Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome
inferredcites →https://doi.org/10.1371/journal.pone.0177459openalex-snapshot
Singularity: Scientific containers for mobility of compute
inferredcites →https://doi.org/10.3389/fcell.2014.00070openalex-snapshot
Integrative workflows for metagenomic analysis
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1093/gigascience/giy072openalex-snapshot
YAMP: a containerized workflow enabling reproducibility in metagenomics research
inferred← citeshttps://doi.org/10.17520/biods.2018211openalex-snapshot
EPPS, a metabarcoding bioinformatics pipeline using Nextflow
inferred← citeshttps://doi.org/10.70239/arsu.2026.t84.n2.12openalex-snapshot
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