MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

By G. Uritskiy, J. DiRuggiero, James Taylor. Microbiome, 2018

2,196 citations recorded by the source corpus.

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. 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. 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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/da7bb852421275ad9b4b3e7c4a2f12c4b5c1fcd0

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Citations in the corpus

Effect of ammonia on anaerobic digestion of municipal solid waste: Inhibitory performance, bioaugmentation and microbiome functional reconstruction (2020, methodology): “different assemblies and binning results were chosen using metaWRAP [39] and finally 26, 21 and 20 MAGs were obtained from metaspades, OPERA-MS and unicycler, respectively.”
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle (2019, methodology): “MetaBAT2 achieved the best performances among single-sample binning tools also in the evaluation performed in the Metawrap paper (Uritskiy et al., 2018), a recent tool for multiple binning.”
A practical guide to amplicon and metagenomic analysis of microbiome data (2020, methodology): “We recommend using a binning pipe-line such as MetaWRAP (Uritskiy et al., 2018) or DAStool (Sieber et al., 2018), which integrate several binning software packages to obtain re ﬁ ned binning results and more complete genomes with less contamination.”