EzCOVID19
A bioinformatics platform for rapid detection, identification and characterization of SARS-CoV-2 virus
What is EzCOVID19?

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 it’s 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.

SARS-CoV-2 in public next-gen sequence data
Metagenomic, metatranscriptomic, RNA-seq and/or isolate (amplicon or enrichment) next-gen sequence data
Check if your sample contains SARS-CoV-2
Supports single-end/paired-end FASTQ raw files from isolate and metagenomic data.
Example Input files
Metagenomic example
Isolate example
Log in required
Please log in to analyze your own samples.
Click here to log in or register if you do not have an account yet.
Analysis ID
Owned by
Data type
Choose a data type.
Metagenomic raw data
In the future, metagenomic inputs will
also include taxonomic profiling.
Isolate raw data
FASTA
Sequence file(s)
Upload a single-end/paired-end sample.
(Size limit per file: 5 GB)
    Created at
    Required fields
    Upload & Analyze
    Status
    We will send a notification to once the analysis completes.
    File 1
    0%
    File 2
    0%
    Assembly Export to FASTA
    Verdict
    (%) reads from the queried dataset classified to the SARS-CoV-2 reference genome covering % of the genomic sequence. The queried dataset covers % of the SARS-CoV-2 genomic sequence. No reads classified as SARS-CoV-2 virus were obtained from the sample. An error occured during the run.
    Information
    Sequencing library
    Total number of reads in the queried dataset
    Number of reads classified to the SARS-CoV-2 genome
    Percentage of reads classified
    Percentage of genome coverage
    Base number of genome coverage
    Total count of covered bases
    Depth
    Coverage
    0
    Assembly
    SNVs
    Reference

    (NC_045512)
    0
    2 K
    4 K
    6 K
    8 K
    10 K
    12 K
    14 K
    16 K
    18 K
    20 K
    22 K
    24 K
    26 K
    28 K
    SNVs
    Export to Excel

    Single-nucleotide variant table showing nucleotide variations between the input assembly and the SARS-CoV-2 reference. (NC_045512.2)

    Nucleotide
    Assembly
    Reference
    Codon
    Assembly
    Reference
    Amino acid
    Assembly
    Reference
    Variant marker

    †: https://www.biorxiv.org/content/10.1101/2020.04.22.055863v1

    Similarity

    Top 100 SARS-CoV2 GISAID* reference genomes similar to the query assembly.

    Top hits
    Alignment position
    Assembly
    Reference
    Alignment coverage (%)
    Assembly
    Reference
    Alignment identity (%)
    SNV position
    Assembly
    Reference
    SNV base
    Assembly
    Reference
    Top hits similarity tree
    0
    8

    *: 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

    Typing based on 41 sites with a variant over 1% in the current global genome data set.

    SNV tree
    0
    8