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 [1].
Variants are called using paftools.js from the minimap2 package and bcftools [2]
and transformed into a fasta alignment. IQ-TREE [3] is used to reconstruct the
phylogeny. Custom scripts utilising ete3 [4] are used to position new isolates
on the tree which are visualised using phylotree.js [5] 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).
- Shank, S. D., Weaver, S. & Kosakovsky Pond, S. L. phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. BMC Bioinformatics 19, 276 (2018).
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.