Ugarcina Perovic Svetlana, Ramji Vedanth, Chong Hui, Duan Yiqian, Maguire Finlay, Coelho Luis Pedro
Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, 38123 Povo, Italy.
Bioinformatics. 2025 May 6;41(5). doi: 10.1093/bioinformatics/btaf173.
Currently available and frequently used tools for annotating antibiotic resistance genes (ARGs) in genomes and metagenomes provide results using inconsistent nomenclature. This makes the comparison of different ARG annotation outputs challenging. The comparability of ARG annotation outputs can be improved by mapping gene names and their categories to a common controlled vocabulary such as the Antibiotic Resistance Ontology (ARO). We developed argNorm, a command line tool and Python library, to normalize all detected genes across six ARG annotation tools (eight databases) to the ARO. argNorm also adds information to the outputs using the same ARG categorization so that they are comparable across tools.
argNorm is available as an open-source tool at: https://github.com/BigDataBiology/argNorm. It can also be downloaded as a PyPI package and is available on Bioconda and as an nf-core module.
目前可用于在基因组和宏基因组中注释抗生素抗性基因（ARG）的常用工具，其提供的结果使用的命名法不一致。这使得不同ARG注释输出的比较具有挑战性。通过将基因名称及其类别映射到通用的受控词汇表，如抗生素抗性本体（ARO），可以提高ARG注释输出的可比性。我们开发了argNorm，这是一个命令行工具和Python库，用于将六个ARG注释工具（八个数据库）中检测到的所有基因标准化为ARO。argNorm还使用相同的ARG分类向输出添加信息，以便它们在不同工具之间具有可比性。
argNorm作为开源工具可在以下网址获得：https://github.com/BigDataBiology/argNorm。它也可以作为PyPI包下载，并且在Bioconda上可用，还作为nf-core模块提供。
