MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.

ABSTRACT: Microbiomes play crucial roles in diverse ecosystems, spanning environmental, agricultural, and human health domains. 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 rea

SUBMITTER: Xia Y 

PROVIDER: S-EPMC12489473 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature