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EzCOVID19 – detect, characterize and sub-type SARS-CoV-2

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Chunlab/EzBiome has a new platform that we developed to cover most of the analysis needed for CoVID. EzCOVID19 focuses on the rapid detection, identification, and characterization of the SARS-CoV-2 virus. We do this by:

  • Allowing you to use multiple sample starting types (i.e. raw metagenomic, metatranscriptomic, RNA-seq, or isolates).
  • Providing you with a consensus genome assembly along with statistics related to genome coverage, depth metrics, and coverage plots with single nucleotide variant (SNV) relative to the reference SARS-CoV-2 genome.
  • Detection of most similar genomes available in the reference databases based on alignment statistics and SNVs, including a maximum likelihood or parsimony-based similarity tree decorated with SNV profiles.
  • Classification or typing of the queried genome using EzBioCloud’s SNP based classification scheme of SARS-CoV-2 variants, including an evolutionary analysis of the detected SARS-CoV-2 type along with other types observed among publicly available SARS-CoV-2 genomes

Get the complete coverage information of the entire viral genome

In addition to the relationship to concurrently circulated publicly available SARS-CoV-2 genomes, EzCOVID19 enables characterization and typing of the entire viral genome, when the user obtains adequate coverage of the genome.

Graph and table with detected variants

See a detailed graphical breakdown of the variants as well as a table format highlighting the calls.

EzCOVID19 identifies the most similar genomes available in the reference databases (i.e., GISAID)

Including a maximum likelihood or parsimony based similarity tree

Obtain classification or typing of the queried genome using EzBioCloud’s SNP based classification scheme of SARS-CoV-2 variants

Including an evolutionary analysis of the detected SARS-CoV-2 type along with other types observed among publicly available SARS-CoV-2 genomes.

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More To Explore

How to download public SRA Run data

Install SRA toolkit on your computer To download any file from the NCBI SRA database, you need to install SRA toolkit software from NCBI SRA Toolkit.

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