Welcome to the COVID-Profiler - a collection of tools which allow users to analyse Sars-Cov-2 sequencing and immunological data.

Profile

This tool takes whole genome sequence data (NGS or assembled sequence) and produces a report on the mutations present.
Profile

Phylogeny

Align multiple sequence and reconstruct a maximum likelihood phylogeny. A tree is produced as well as several intermediate files.
Reconstruct

Diagnostics

Check conservation of primer binding sites across the timeline of the pandemic and in different geographic regions through interactive plots
Analyse
Get in touch
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.
Pipeline
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.
  1. Li, H. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
  2. 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).
  3. 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
  4. Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol. Biol. Evol. 33, 1635–8 (2016).
  5. 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).
Disclaimer
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.