Download Consensus Genome Data

Jump to Section:

• Download Data for a Single Genome
• Download Data for One or Multiple Genomes
• Available Intermediate Files
• Note on Data Submission to NCBI

Overview

You can easily download virus consensus genome data, including consensus genome sequences (FASTA format) and intermediate files produced throughout the pipeline. Here we outline steps to download consensus genome data.

After reading this guide, you will:

• Learn different options for downloading consensus genome data
• Become familiar with available intermediate files

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Download Data for a Single Consensus Genome

You can download data for a single consensus genome from the Sample Report page. Here you can download the consensus genome sequence and generated intermediate files in a single folder.

To download a folder with consensus genome data:

1. Navigate to the Consensus Genome tab for the sample and select the genome of interest from the dropdown menu (if multiple genomes have been assembled).
2. To download all the data associated with the selected consensus genome, click the "Download All” button on the right-hand side of the page.

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Download Data for One or Multiple Consensus Genomes 

You can download data for a single or multiple consensus genomes at the same time (bulk download) from the Consensus Genome tab for a project of interest. From this tab you can download the consensus genome sequence, assembly metrics, sample metadata, and intermediate files. Download files will be created and stored in your Downloads page. Please note that files available through the Downloads page will be deleted after 7 days of creating the download. 

To download consensus genome files of interest:

1. Navigate to the Consensus Genomes tab found on the Project page of interest.
2. Click the Download icon on the right-hand side of the page and select the download type of interest from the dialog box.
3. Go to the Downloads page to view download status and download files.

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Available Intermediate Files

You can download Intermediate files, including mapping information contained within BAM files, to troubleshoot genome quality issues that may need to be evaluated and submit data to public repositories. Below we describe available intermediate files for download through the Sample or Project pages for consensus genomes.

Note: BAM and VCF files can be viewed using the freely available Integrative Genomics Viewer (IGV), which includes a Web App for analyzing genomes online.

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Note on Consensus Genome Data Submission to NCBI

Downloaded data can be submitted to NCBI’s public repositories for the benefit of the broader scientific community. Consensus genomes can be submitted to GenBank, whereas reads (non-host reads) and BAM files can be submitted to the Sequence Read Archive (SRA). Click here for an overview of how to submit sequence data to NCBI.