argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)
Ugarcina Perovic, Svetlana, Ramji, Vedanth, Chong, Hui, Duan, Yiqian, Maguire, Finlay, & Coelho, Luis Pedro (2024) argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO). [Preprint] (Unpublished)
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ARGNORM Preprint (Ugarcina Perovic Ramji et al 2024). Available under License Creative Commons Attribution 4.0. |
Description
Motivation: Currently available and frequently used tools for annotating antimicrobial 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).
Results: We developed argNorm, a command line tool and Python library, to normalize all detected genes across 6 ARG annotation tools (8 databases) to the ARO. argNorm also adds information to the outputs using the same ARG categorization so that they are comparable across tools.
Availability and implementation: 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.
Impact and interest:
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| ID Code: | 252448 | ||
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| Item Type: | Working Paper (Preprint) | ||
| Refereed: | No | ||
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| Measurements or Duration: | 9 pages | ||
| DOI: | 10.5204/rep.eprints.252448 | ||
| Pure ID: | 178903178 | ||
| Divisions: | Current > QUT Faculties and Divisions > Faculty of Health Current > Schools > School of Biomedical Sciences |
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| Funding Information: | Australian Research Council FT230100724, International Development Research Centre 109304-001, NHMRC 20311902, Science and Technology Commission of Shanghai Municipality, 2018HZDZX01 | ||
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| Copyright Owner: | 2024 The authors | ||
| Copyright Statement: | This work is covered by copyright. Unless the document is being made available under a Creative Commons Licence, you must assume that re-use is limited to personal use and that permission from the copyright owner must be obtained for all other uses. If the document is available under a Creative Commons License (or other specified license) then refer to the Licence for details of permitted re-use. It is a condition of access that users recognise and abide by the legal requirements associated with these rights. If you believe that this work infringes copyright please provide details by email to [email protected] | ||
| Deposited On: | 10 Oct 2024 00:40 | ||
| Last Modified: | 09 Feb 2025 14:46 |
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