Quick Guide to SARS-CoV-2 Genome Assembly

Overview

Here we describe general steps to assemble SARS-CoV-2 consensus genomes within CZ ID. 

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SARS-CoV-2 Genome Assembly Steps

To assemble SARS-CoV-2 genomes:

1) Log in to your CZ ID account.

2) Go to the Upload page from the Discovery page by selecting the "Upload" link by your username. Follow prompts to add SARS-CoV-2 consensus genome data and review information to be uploaded. For detailed steps on how to upload data see:

• Upload Data and Assemble SARS-CoV-2 Genomes

1. Upload Page: Click link to navigate to the Upload page.
2. Upload Steps: The upload process is divided into three general sections (Samples, Metadata, and Review). The current section will be highlighted in blue.

3) Go to the Project page after uploading samples to view sample run status. The sample run should be listed under the Consensus Genomes tab.

1. Project Name: Indicates you are viewing the project's page.
2. Run Status: Indicates if the run has been completed, completed with issue, or failed.
3. Consensus Genome Tab: Select the consensus genome tab to view assembly or sample run status. 

4) Once the sample run is completed, click on the sample to view the Consensus Genome Report. The report includes genome assembly metrics and a coverage plot.

1. Sample Name
2. Assembly Metrics
3. Coverage Stats
4. Coverage Visualization

5) Assess the quality of the genome and download data.