Welcome to the COVID-Profiler - a collection of tools which allow users
to analyse Sars-Cov-2 sequencing and immunological data.
This work was made possible through a great collaborative effort.
We welcome any suggestions or contributions, so do not hesitate to
get in touch with Jody Phelan
or Wouter Deelder
. The project is completely open source and the links to
the source code is available below.
Sequences are aligned to the reference genome (NC_045512.2) using minimap2 .
Variants are called using paftools.js from the minimap2 package and bcftools 
and transformed into a fasta alignment. IQ-TREE  is used to reconstruct the
phylogeny. Custom scripts utilising ete3  are used to position new isolates
on the tree which are visualised using phylotree.js  in the web browser.
Sample data is downloaded from NCBI nucleotide database using Entrez Direct
The website is built using flask
All the code is available from https://github.com/jodyphelan/covid-profiler
- Li, H. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
- Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).
- Minh, B. Q. et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. (2020). doi:10.1093/molbev/msaa015
- Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol. Biol. Evol. 33, 1635–8 (2016).
This tool is for Research Use Only. It has not been approved, cleared,
or licensed by any regulatory authority. By submitting sequence data the
user acknowledges no intended medical purpose or objective such as
clinical diagnosis, patient management, or human clinical trials.