HDR UK - Resources for 🦠COVID-19 Research

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

A selenium spider for GISAID

This project tries to give a glimpse of the different variants of SAR-CoV-2 in the world.

VariantHunter is a tool for fast detection of emerging SARS-CoV-2 variants. It's an highly flexible and user friendly application for the systematic monitoring of the evolution of SARS-CoV-2 both at global and regional level.

Processing GISAID SARS-CoV-2 emerging variants data and generating a language model using Transformers. The model semantically captures masked glycoprotein amino acid mutations in emerging variants of the SARS-CoV2-virus and gives appropriate scores for each potential aa change.

Access the GISAID Flu database using Python

This tool can be used to download the samples and metadata from GISAID provided you have an existing account with download privileges.

Assisted download of selected samples from GISAID

This repo summarises the data sources, web application, tools and reviews paper of SARS-Cov-2. Trace the study progress of SARS-Cov-2 based on GISAID data.

Repository with codes to the paper 'Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the United States'

Utility to retrieval metadata from GISAID EPI_SET URL

A tool to filter the full fasta sequences from GISAID.

ShinyApp repo for the CovidTracker, any details further than the codes here available please send an email to rafael.lopes at yale.edu

Lab-Specific Bias FILter (LSBFILT)

Simple Discord bot that scrapes GISAID SARS-CoV-2 variant frequencies

R package for entropy-informed detection of emerging viral variants and genomic surveillance. Implements per-site Shannon entropy, Gaussian mixture model site selection, Hellinger distance, and non-parametric change-point detection. Validated on SARS-CoV-2 Spike protein sequences from NCBI and GISAID databases.