MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
Open accessPublished version of a preprint
Abstract
BACKGROUND: The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization. RESULTS: To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization. CONCLUSIONS: MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP .
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Whole genomes of organisms, in addition to strain tracking, can be extracted from shotgun metagenomic data, allowing for evolutionary analysis of specific organisms associated with a particular disease or environment.
“Whole genomes of organisms, in addition to strain tracking, can be extracted from the data, allowing for evolutionary analysis of specific organisms associated with a particular disease or environment.79, 80, 81”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [80]
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- Authors
- Uritskiy, G. V., DiRuggiero, J., & Taylor, J.
- Affiliations
- Johns Hopkins University (US)
- Corresponding author
- DiRuggiero, Jocelyne
- Taylor, James
- Venue
- Microbiome
- Published
- 2018-09-15
- Volume
- 6
- Issue
- 1
- Pages
- 158-158
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC6138922
- OpenAlex
- W2950464960
- Cited by
- 2,642
- References
- 52
- Citations by year
- 2026: 499 · 2025: 598 · 2024: 497 · 2023: 368 · 2022: 286 · 2021: 239 · 2020: 116 · 2019: 34 · 2018: 4 · 2012: 1
- FWCI
- 37.42
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Microbiome (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Aeronautics and Space Administration (NNX15AP18G, NNX15AK57G)
- National Science Foundation (DEB1556574)
- National Human Genome Research Institute (HG006620)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- metagenome binning, genome-resolved metagenomics, metagenome-assembled genomes
- MeSH terms
- Gastrointestinal Microbiome, Data Analysis, Algorithms, Bacteria, Humans, Software, Genome, Bacterial, Metagenome, Metagenomics, Data Mining
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