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However, in-depth metagenomic data analysis presents significant technical and resource challenges, particularly at scale. Existing computational pipelines are typically limited to either reference-based or reference-free approaches and exhibit inefficiencies in process large datasets. Here, we introduce MetaflowX (https:\/\/github.com\/01life\/MetaflowX), an open-resource workflow integrating both analytical paradigms for enhanced metagenomic investigations. This modular framework encompasses short-read quality control, rapid microbial profiling, hybrid contig assembly and binning, high-quality metagenome-assembled genome (MAG) identification, as well as bin refinement and reassembly. Benchmarking tests showed that MetaflowX completed full metagenomic analyses up to 14-fold faster and with 38% less disk usage than existing workflows. It also recovered the highest number of high-quality and taxonomically diverse MAGs. A dedicated reassembly module further improved MAG quality, increasing completeness by 5.6% and reducing contamination by 53% on average. Functional annotation modules enable detection of key features, including virulence and antibiotic resistance genes. Designed for extensibility, MetaflowX provides an efficient solution addressing current and emerging demands in large-scale metagenomic research.<\/jats:p>","DOI":"10.1093\/nar\/gkaf954","type":"journal-article","created":{"date-parts":[[2025,9,22]],"date-time":"2025-09-22T11:26:44Z","timestamp":1758540404000},"source":"Crossref","is-referenced-by-count":4,"title":["MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis"],"prefix":"10.1093","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0765-6606","authenticated-orcid":false,"given":"Yan","family":"Xia","sequence":"first","affiliation":[{"name":"01Life Institute , Shenzhen\u00a0 518100 ,","place":["China"]},{"name":"Shen 1001 Life Institute , Shanghai\u00a0 200435 ,","place":["China"]},{"name":"State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University , Nanjing\u00a0 210093 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1904-1158","authenticated-orcid":false,"given":"Lifeng","family":"Liang","sequence":"additional","affiliation":[{"name":"01Life Institute , Shenzhen\u00a0 518100 ,","place":["China"]},{"name":"Shen 1001 Life Institute , Shanghai\u00a0 200435 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaokai","family":"Wang","sequence":"additional","affiliation":[{"name":"01Life Institute , Shenzhen\u00a0 518100 ,","place":["China"]},{"name":"Shen 1001 Life Institute , Shanghai\u00a0 200435 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zixiang","family":"Chen","sequence":"additional","affiliation":[{"name":"01Life Institute , Shenzhen\u00a0 518100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Yuncheng University , Yuncheng, Shanxi 044000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Yang","sequence":"additional","affiliation":[{"name":"01Life Institute , Shenzhen\u00a0 518100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hailiang","family":"Xie","sequence":"additional","affiliation":[{"name":"01Life Institute , Shenzhen\u00a0 518100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhimin","family":"Ding","sequence":"additional","affiliation":[{"name":"01Life Institute , Shenzhen\u00a0 518100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoting","family":"Huang","sequence":"additional","affiliation":[{"name":"01Life Institute , Shenzhen\u00a0 518100 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