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COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data
Jody Phelan1, Wouter Deelder2,3, Daniel Ward2
1Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK. jody.phelan@lshtm.ac.uk.
Background:
SARS-CoV-2 virus sequencing has been applied to track the COVID-19 pandemic spread and assist the development of PCR-based diagnostics, serological assays, and vaccines. With sequencing becoming routine globally, bioinformatic tools are needed to assist in the robust processing of resulting genomic data.
Results:
We developed a web-based bioinformatic pipeline ("COVID-Profiler") that inputs raw or assembled sequencing data, displays raw alignments for quality control, annotates mutations found and performs phylogenetic analysis. The pipeline software can be applied to other (re-) emerging pathogens.
Conclusions:
The webserver is available at http://genomics.lshtm.ac.uk/ . The source code is available at https://github.com/jodyphelan/covid-profiler .
