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
- Python Flask
- Leaflet for Map View
- GeoTools for WGS84-OSGB36 conversions
- Map data: OpenStreetMap and MapBox
- Tree presentation: Phylotree Javascript library
- Tree building: iqtree
- Search a sample and show the related herd on the map
- Show sample related cattle movements on the map
- Search genetic neighbourhood of a sample and show all herds on the map
- Cohabitation records of a genetic neighbourhood
- Phylogeny tree of a sample in a 3-snp cluster
- Quality data of a sample (reads coverage and ACGT percentage)
- Within herd SNP Distance Matrix
- Cluster all sample based on their genetic distance and show them on the map
- View sub-cluster within a cluster on the map
- Interesting score: sample pairs that are far apart in miles but close in genetic SNPs.