Benchmarking Results of Metagenomic Pipelines across Diverse Microbiomes

This repository provides the complete assembly and binning outputs from a comparative genome-resolved metagenomic analysis of four microbiome environments: gut, sewage, air, and a simulated dataset. In addition to the primary results, the repository includes all materials required for full reproducibility and independent re-analysis, including: Benchmarking/ – pipeline execution scripts, sample sheets, and trace reports for nextflow piplines (MetaBolt & nf-core/mag) Visualization/ – Python scripts used to generate all figures and plots DAG view of MetaBolt workflow in PNG file Each dataset was processed using three established genome-resolved metagenomic pipelines: MetaBolt – A computationally efficient, Nextflow-based pipeline that uses an optimized reduced k-mer strategy for fast and scalable recovery of metagenome-assembled genomes (MAGs). MetaWRAP – A widely used modular framework for metagenomic binning, refinement, and genome reconstruction. nf-core/mag – A community-curated, Nextflow-based workflow implementing best-practice standards for metagenomic assembly, binning, and quality assessment. This dataset is designed to enable transparent, reproducible benchmarking and quantitative performance comparison of state-of-the-art metagenomic assembly and binning pipelines across diverse environmental microbiomes. 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