Variant analysis and visualization

Title	URL	Features
Nextstrain SARS-CoV-2 resources	https://nextstrain.org/ncov	Interactive phylogeographic visualization of SARS-CoV-2 genomic evolution and epidemic spread Includes global as well as various regional-level analyses (by continents, countries, etc.) Shows distribution of both nucleotide and amiono acid mutations across the viral genome Data derived from GISAID
COG-UK: COV-GLUE	http://cov-glue.cvr.gla.ac.uk/#/home	Powered by GISAID, provides a database for amino acid variations Based on GLUE (Genes Linked by Underlying Evolution), a data-centric bioinformatics environment for virus sequence data Allows users to submit their own sequneces (FASTA files) for phylogenetic placement and genome visualiation
COG-UK: Microreact	https://microreact.org/project/COGconsortium	Continuous evaluation of the viral lineages circulating in the UK Each unique viral sequence and its frequency can be traced through time and space using interactive map and phylogeny
SARS-CoV-2 Alignment Screen	https://macman123.shinyapps.io/ugi-scov2-alignment-screen/	Visualization tool providing the distribution of SNPs and homoplasies across the genome Tree can be pruned by sampling locations Data derived from GISAID; latest update, 04/06/2020 Published in: https://doi.org/10.1016/j.meegid.2020.104351
COVID-19 Viral Genome Analysis Pipeline	https://cov.lanl.gov/content/index	A collection of tools for analyzing and visualizing mutations of interest in the spike (e.g., Spike 614) and other proteins Includes geographic and phylogenetic distribution, variant accumilatoion over time, sequence locator, etc. Data drawn from GISAID Published in: https://doi.org/10.1016/j.cell.2020.06.043
CNCB/NGDC Genome Variations	https://ngdc.cncb.ac.cn/ncov/variation	Visualizes the distribution and statistics calculated from SARS-CoV-2 strains compared against a reference genome Contains also spatiotemporal dynamics, phylogeny, and haplotype network analyses Part of CNCB/NGDC Resource for Coronavirus 2019 (RCoV19)