EzCOVID19 is a cloud-based bioinformatics platform for rapid detection, identification and characterization of SARS-CoV-2 virus from raw metagenomic, metatranscriptomic, RNA-seq and/or isolate (amplicon or enrichment) next-gen sequence data suspected of containing the SARS-CoV-2 virus. EzCOVID19 provides scientists with a consensus genome assembly along with statistics related to genome coverage, depth metrics and coverage plots relative to the reference SARS-CoV-2 genome.
Furthermore, to deliver additional insight into the nature of this virus as well as its origin, evolution and relationship to concurrently circulated publicly available SARS-CoV-2 genomes, EzCOVID19 offers characterization and typing of the entire viral genome when adequate coverage of the genome is obtained. It provides Single Nucleotide Variant (SNV) information, including a graph and table with detected variants in the SARS-CoV-2 genome, identifies most similar genomes available in the reference databases (i.e., GISAID) based on alignment statistics and SNVs, including a maximum likelihood or parsimony based similarity tree decorated with SNV profiles, and offers 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.
(NC_045512)
Single-nucleotide variant table showing nucleotide variations between the input assembly and the SARS-CoV-2 reference. (NC_045512.2)
†: https://www.frontiersin.org/articles/10.3389/fmicb.2020.01800/full
Top 100 SARS-CoV2 GISAID* reference genomes similar to the query assembly.
*: Shu, Y., McCauley, J. (2017) GISAID: Global initiative on sharing all influenza data – from vision to reality. EuroSurveillance, 22(13) doi:10.2807/1560-7917.ES.2017.22.13.30494 PMCID: PMC5388101
Typing based on 41 sites with a variant over 1% in the current global genome data set.