ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization.

ABSTRACT: Antibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens. A number of computational pipelines are available and under development to support environmental ARG monitoring; the pipeline we present here is promising for general adoption for the purpose of harmonized global monitoring. Specifically, ARGem is a user-friendly pipeline that provides full-service analysis, from the initial DNA short reads to the final visualization of results. The capture of extensive metadata is also facilitated to support comparability across projec

SUBMITTER: Liang X 

PROVIDER: S-EPMC10558085 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature