amrnet Goto Github PK

• Description
• Installation
• User guide
• Citing
• Funding & acknowledgements

The AMRnet dashboard aims to make high-quality, robust and reliable genome-derived AMR surveillance data accessible to a wide audience. Visualizations are geared towards showing national annual AMR prevalence estimates and trends, that can be broken down and explored in terms of underlying genotypes and resistance mechanisms. We do not generate sequence data, but we hope that by making publicly deposited data more accessible and useful, we can encourage and motivate more sequencing and data sharing.

We started with Salmonella Typhi, built on our TyphiNET dashboard which uses data curated by the Global Typhoid Genomics Consortium (to improve data quality and identify which datasets are suitable for inclusion) and analysed in Pathogenwatch (to call AMR determinants and lineages from sequence data). More organisms will be added throughout 2024-25, using data sourced from analysis platforms such as Pathogenwatch, Enterobase, and potentially others.

Visiting the AMRnet dashboard for more informations.

Note: While installing MongoDB, check the option to install MongoDB Compass. If there's no option, you can download it here: MongoDB Compass

npm install -g yarn

git clone https://github.com/amrnet/amrnet

npm install

MONGO_URI= (see item 7 from the manual)
MONGO_URI_ATLAS=(see item 7 from manual to access MongoDB Atlas cloud)

yarn start: prod

If you use data/metadata from the AMRnet dashboard, or the analysis based on these data, please cite:

DOI: https://zenodo.org/doi/10.5281/zenodo.10810218 GitHub: https://github.com/amrnet/amrnet/

AMRnet is funded by the Wellcome Trust and based in Kat Holt's group at the London School of Hygiene and Tropical Medicine.