Gene Surfing: An efficient and versatile tool for targeted enzyme mining in metagenomics.

ABSTRACT: Microbial community studies have established enzymes' pivotal catalytic roles in ecosystem metabolism, yet cultivation-dependent methods fail to exploit uncultured microbial enzyme resources. Metagenomics overcomes this by directly accessing microbial genetic information, but its massive data generation challenges precise enzyme identification: (1) Restricted applicability across varied sample types. (2) Narrow functional scope in target enzyme discovery. To address this, we developed Gene Surfing, a bioinformatics workflow platform based on Snakemake. It integrates modules for data quality control (Fastp), genome assembly (MEGAHIT), assembly evaluation (QUAST and MetaQUAST), functional annotation (Prokka), and homologous sequence retrieval (MMseqs2). Gene Surfing offers scalability, repro

SUBMITTER: Xu T 

PROVIDER: S-EPMC12396413 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature