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 .
Keywords: NGS; Phylogenetics; Sars-Cov-2; Sequencing.
© 2022. The Author(s).