Upload Data and Assemble SARS-CoV-2 Genomes Using the Web App

Overview

You can easily assemble SARS-CoV-2 consensus genomes through CZ ID. Here we list steps to upload data to the SARS-CoV-2 consensus genome pipeline, where you can assemble short- (Illumina) and long-read (Nanopore) data. See SARS-CoV-2 Pipeline for details about pipelines used to assemble SARS-CoV-2 genomes.

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Upload SARS-CoV-2 data

To upload data and view assembled genome:

1. Click "Upload" in the upper right corner of your screen to go to the Upload Samples page within your CZ ID account.
2. Select the project where you would like to upload the data or create a new project.
3. Select “SARS-CoV-2 Consensus Genome” for analysis type.  The typical CZ ID pipeline to analyze metagenomic data will not be run. Only the selected SARS-CoV-2 consensus genome pipeline will run.
4. Select the sequencing platform and wet-lab protocol used to obtain SARS-CoV-2 data. The pipeline supports data generated with Illumina and Nanopore sequencing platforms. Picking the correct wet-lab protocol is a critical step because the protocol chosen dictates the primers that will be removed during genome assembly. 
5. If you are using Nanopore, choose the correct Medaka model for the best results. 
   1. 1. • Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION or PromethION), iii) the base caller variant, and iv) the base caller version
         • There is a default consensus genome medaka model: r941_min_high_g360, which can be used if you are unsure of which medaka model to select.
         •  Where a version of Guppy has been used without an exactly corresponding medaka model, the medaka model with the highest version equal to or less than the guppy version should be selected.
         • Use the flow chart below to choose the correct Medaka model (click here if you can't see the figure below).

If you're having trouble viewing the above diagram, click here.

6. Upload your sequence files and click "Continue" to go to the Metadata page.

7. Fill in metadata fields and click "Continue" to go the Review page.

8. Review the information, accept CZ ID Terms of Service and "Start Upload".

9. A pop up will appear to indicate the sample upload progress. Click "Go to Project" to view sample status.

10. You will see the status of your sample under the Consensus Genome tab for the project of interest under My Data page.

11. Once the sample run is "complete", click on the sample name to view the assembled genome.

12. Assess the quality of the genome and download data.