> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/resfinder.md).

# Resfinder

## About

[Resfinder](http://genepi.food.dtu.dk/resfinder) is developed by the Centre for Genomic Epidemiology. Pathogenwatch integrates the Resfinder software for AMR gene and variant detection for the species shown in the table below. If one is available, the species or genus-specific library is used. In some cases, modifications are made to the Resfinder database, either to mask markers that are not informative or to add an antibiogram where one isn't provided.

## Method

For full details on the Resfinder method see the software repository at <https://bitbucket.org/genomicepidemiology/resfinder/src/master/>. Modifications are applied directly to the database during integration into Pathogenwatch. Details on modifications can be found in the repository: <https://github.com/pathogenwatch/tasks/tree/main/resfinder/rfplus/mod_files>

## How to cite

ResFinder 4.0 for predictions of phenotypes from genotypes.\
Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AR, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykasenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. Journal of Antimicrobial Chemotherapy. 2020 Aug 11.\
PMID: 32780112 doi: 10.1093/jac/dkaa345


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