Centriflaken: An automated data analysis pipeline for assembly and in silico analyses of foodborne pathogens from metagenomic samples.

ABSTRACT: Rapid and comprehensive analysis of metagenomic data from samples associated with foodborne outbreaks is of critical importance in food safety. Equally important is the need for automated analysis pipelines that allow the rapid and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking from metagenomic data. Here, we present centriflaken, an automated precision metagenomics pipeline for detecting and characterizing Shiga toxin-producing Escherichia coli (STEC) from metagenomic data. centriflaken streamlines the process of generating metagenome-assembled genomes (MAGs) and conducting in silico analyses of STECs, significantly reducing the time and manual effort required for comprehensive pathogen profiling. centriflaken was validated using Oxford

SUBMITTER: Konganti K 

PROVIDER: S-EPMC12725755 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature