COVID-Profiler

Phelan, JORCID logo and Deelder, W (2020). COVID-Profiler. [Dataset]. Github. https://github.com/jodyphelan/covid-profiler
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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

Coronavirus, COVID-19

Item Type Dataset
Capture method Aggregation
Date 2020
Language(s) of written materials English
Creator(s) Phelan, JORCID logo 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

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