Benchmarking Results of Metagenomic Pipelines across Diverse Microbiomes

This repository contains assembly and binning results generated from metagenomic analyses of four distinct microbiome environments: gut, sewage, air, and a simulated dataset. Each dataset was analyzed using three genome-resolved metagenomic pipelines: MetaBolt – A computationally efficient, Nextflow-based pipeline employing an optimized set of k-mers for rapid and scalable recovery of metagenome-assembled genomes (MAGs). MetaWRAP – A widely adopted modular pipeline designed for comprehensive metagenomic binning and genome reconstruction. nf-core/mag – A community-curated, Nextflow-based pipeline for reproducible metagenomic assembly, binning, and quality assessment following best practices. This dataset is intended to support reproducible benchmarking and comparative performance evaluation of metagenomic assembly and binning workflows. Microbiome Datasets The following publicly available datasets were used: Gut Microbiome – NCBI BioProject: PRJNA945504 Sewage Microbiome – NCBI BioProject: PRJNA1020581 Air Microbiome – NCBI BioProject: PRJNA486429 Simulated Microbiome – CAMI II Toy Human Gut Metagenome dataset Each dataset contains 10 representative samples, processed with MetaBolt, MetaWRAP and nf-core/mag using identical inputs. Citation If you use this dataset or any part of it in your work, please cite the following resources accordingly: MetaBolt: MetaBolt: A Computationally Efficient Pipeline for the Rapid Recovery of Metagenome-Assembled Genomes, 2025.Zenodo DOI: https://doi.org/10.5281/zenodo.15243430 MetaWRAP: MetaWRAP – a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018;6:158.DOI: https://doi.org/10.1186/s40168-018-0541-1 nf-core/mag: nf-core/mag: Metagenome Assembly and Binning Pipeline. nf-core, 2020.DOI: https://doi.org/10.5281/zenodo.3589523