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This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user\u2010friendly pipeline that supports multiple analysis methods, including quality control and host removal, read\u2010based, assembly\u2010based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third\u2010generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/YongxinLiu\/EasyMetagenome\">https:\/\/github.com\/YongxinLiu\/EasyMetagenome<\/jats:ext-link>.<\/jats:p>","DOI":"10.1002\/imt2.70001","type":"journal-article","created":{"date-parts":[[2025,2,14]],"date-time":"2025-02-14T14:35:56Z","timestamp":1739543756000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":52,"title":["EasyMetagenome: A user\u2010friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research"],"prefix":"10.1002","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-7762-7199","authenticated-orcid":false,"given":"Defeng","family":"Bai","sequence":"first","affiliation":[{"name":"Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 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