Phelan, J and Deelder, W. 2020. COVID-Profiler. [Online]. Github. Available from: https://github.com/jodyphelan/covid-profiler
Phelan, J and Deelder, W. COVID-Profiler [Internet]. Github; 2020. Available from: https://github.com/jodyphelan/covid-profiler
Phelan, J and Deelder, W (2020). COVID-Profiler. [Data Collection]. Github. https://github.com/jodyphelan/covid-profiler
Description
Welcome to the COVID-Profiler - a pipeline which allows users to analyse Sars-Cov-2 sequencing data to place isolates within a real-time tree. Every hour, all publically available sequences from the current COVID-19 outbreak are downloaded and a maximum likelihood tree is built. Users can upload their own sequences to look where they are positioned on the tree. The pipeline searches for SNPs associated with branches on the tree. It then uses the variants to find the closest neighbours on the tree. In parallel it classifies the strains into S/L types as defined by Tang et al.
Keywords
| Data capture method | Aggregation |
|---|---|
| Date (Date submitted to LSHTM repository) | 2020 |
| Language(s) of written materials | English |
| Data Creators | Phelan, J and Deelder, W |
|---|---|
| Research Group | The Applied Genomics Centre |
| Participating Institutions | London School of Hygiene & Tropical Medicine, London, United Kingdom |
| Date Deposited | 28 Apr 2020 14:26 |
|---|---|
| Last Modified | 07 Jun 2022 16:53 |
| Publisher | Github |
