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COVID-19 Viral Genome Analysis Pipeline
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Site Map

Site Map of the SARS-CoV-2 Analysis Pipeline

 

Curated Information

Spike Variants: Updates and Annotation A list of our curated analyses of Spike variants, both current and past versions. These files include:

  • Curated List of Common Spike Variants (.xlsx) an excel table detailing Spike variants of interest and concern
  • Variants README file (.doc) explanatory information to accompany the Curated List of Common Spike Variants
  • Notes on Specific Variants (.pdf)

Variant Color Key The color key for representing common variants, as used by several of the tools and resources on this website. This link accesses the most recent version.

All Curated Information A list of all curated information, current and past versions.

Resources

Most common spike forms based on Pango lineage designations A list of Pango-defined Spike lineages, showing the number of such sequences and the associated mutations.

Embers A graph showing overall global trends in variant frequency over the past year.

Geographic distribution of hCoV-19 variants View pie charts of variant distribution per country, displayed on a global map.

SHIVER SARS CoV-2 Historically Identified Variants in Epitope Regions. SHIVER identifies sets of variant forms of SARS CoV-2 with a focus on just the NTD and RBD neutralizing antibody epitope regions of the Spike protein.

Tables of mutating sites in Spike Automated summary of the most common amino acid variants in Spike, updated daily.

XSPIKE eXplore the SPIKE protein sequence in the SARS CoV-2 virus.

Tools

AnalyzeAlign Show weblogos, calculate frequency by position, and find variants in an alignment.

Geographically Restricted Embers Follow emergent SARS-CoV-2 variants over time.

Geographically Restricted SHIVER View SARS CoV-2 historically identified variants in a geographic region.

Geographically Restricted XSPIKE eXplore the SPIKE protein sequence in the SARS CoV-2 virus. Choose a geographic region and time period of interest.

Isotonic Regression Model the daily fraction of a SARS-CoV-2 variant as a function of time in local regions.

Relative Frequency Change By Geographical Region Use contemporary GISAID data to identify adequately sampled geographical regions and to determine which of those regions are experiencing a significant shift (either up or down) in relative frequency of specific variants.

SARS-CoV-2 Sequence Locator Find the position of your nucleotide or protein sequence(s) relative to the appropriate viral reference strain; or obtain a sequence based on a coordinate location.

Tables of mutating sites Create a table of the amino acid variants in any CoV protein, based on your own choice of date range and geographic region.

Tracking Mutations List changes and correlated mutations at specific positions. Output can be limited to specific lineages, date ranges, and geographic regions.

COV Variant Visualizer Make a highlighter plot showing mutated positions in an alignment.

External Tools Links to CoV

 

last modified: Wed Oct 6 14:08 2021



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