COVID-19 workspaces, data and tools in Terra

Anton Kovalsky

In an effort to slow the impacts of the 2019 novel coronavirus (COVID-19), the Terra team and our scientific collaborators are working as quickly as possible to make data and tools for COVID-19 analysis available in Terra. 

We will maintain this article in the support center as an orientation to COVID-19-related public resources in Terra as well as the educational materials to help you learn how to use them. 

If you are new to Terra, welcome!  Here’s how to get started.

Before diving into a workspace to analyze COVID-19 data, you might need to get acquainted with Terra and what you need to know to work securely and collaboratively here.

Discover COVID-19 data and tools in Terra workspaces

Workspaces allow you to get hands-on experience with COVID-19-related data and analyses. After registering for Terra, select the workspace links below to start analyzing COVID-19 data! The workspaces below include viral genomic analyses and single-cell analyses.

Viral genomics analyses

Review best-practices and workflows for processing raw viral genomic sequencing data as featured in this preprint. This workspace includes workflows for assembling viral genomes, running results against the Kraken taxonomic classifier, and building trees to analyze phylogeny and evolutionary relationships using the Nextstrain tool Augur

An overview of the workspace tools is shown below. You can read more details about the workspace in this blog and this blog. You can also view a video tutorial for this workspace on our youtube channel.

Reproduce a high-resolution view of the viral genomics data used by the Broad Institute's Viral Genomics group to track the introduction and spread of SARS-CoV-2 in the Greater Boston area (see the preprint). These data include:

    • High-quality viral genomes sequenced from nasopharyngeal swabs from individuals with confirmed SARS-CoV-2 infection from MGH and the MA DPH
    • Over 5,000 viral genomes from GenBank that can be used to build NextStrain phylogenetic trees with your data

In this workspace, you will also learn how to submit your own batch sequencing data to GenBank using a convenient workflow. The steps are outlined below. Read more about the workspace in this blog.

newoverview_1.png

Single-cell analyses

Use Jupyter Notebooks to fully reproduce the cross-tissue single-cell analyses in this preprint which assesses cell-type-specific expression of ACE2, TMPRSS2, and CTSL, mediators of SARS-CoV cellular entry.

Explore Single Cell Portal for COVID-19-related research and data

The Single Cell Portal offers a COVID-19 page dedicated to collecting single-cell analysis studies that have been identified by their authors as being potentially relevant to COVID-19 research. These studies provide insights into key topics such as the lung's inflammatory response to respiratory viruses and the expression of the COVID-19 receptor (ACE2) and associated protease (TMRSS2). 

Single Cell Portal (SCP) is a portal built on top of Terra to facilitate sharing single-cell analysis research results through user-friendly interactive visual displays. To find out more about Single Cell Portal, see the SCP wiki.

Read blogs highlighting the latest COVID-19 research in Terra

Read preprints highlighting COVID-19 research in Terra

The following are preprint manuscripts that accompany the COVID-19 workspaces.

Find additional Broad COVID-19 resources

Read how the Broad community is responding to COVID-19 and learn about how different Broad teams have developed resources related to:

Was this article helpful?

1 out of 1 found this helpful

Have more questions? Submit a request

Comments

1 comment

  • Comment author
    Andrew Cherniack

    Will Terra be providing free credits to scientists world wide who want to do COVID19 analysis?  With the on-going crisis, it seems like the right thing to do.

    0

Please sign in to leave a comment.