ViewBovine is a Web Portal for exploring WGS data of M.bovis, linking genetic relatedness with geographical neighbourhood for understanding bTB transmission.

pip3 install -r requirements

git clone https://github.com/oxfordfun/ViewBovine
cd ViewBovine
APP_SETTINGS='config.SwanseaProductionConfig' python3 main.py

1. Python Flask
2. Leaflet for Map View
3. GeoTools for WGS84-OSGB36 conversions
4. Map data: OpenStreetMap and MapBox
5. Tree presentation: Phylotree Javascript library
6. Tree building: iqtree

1. Search a sample and show the related herd on the map
2. Show sample related cattle movements on the map
3. Search genetic neighbourhood of a sample and show all herds on the map
4. Cohabitation records of a genetic neighbourhood
5. Phylogeny tree of a sample in a 3-snp cluster
6. Quality data of a sample (reads coverage and ACGT percentage)
7. Within herd SNP Distance Matrix
8. Cluster all sample based on their genetic distance and show them on the map
9. View sub-cluster within a cluster on the map
10. Interesting score: sample pairs that are far apart in miles but close in genetic SNPs.