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.
The resources in this article include:
- Support for getting started with Terra
- COVID-19-related Terra workspaces
- COVID-19 research and data in Single Cell Portal
- Blogs highlighting COVID-19 research in Terra
- Preprints highlighting COVID-19 research in Terra
- Additional Broad community COVID-19 resources
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.
- Overview for new users
- How to set up a Terra account
- An overview of navigating the Terra interface
- An introduction to Terra workspaces
- Instructions for uploading your own data to Terra
- An introduction to running workflows on Terra
- Instructions for launching a customized virtual machine for downstream analysis
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.
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.
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
- (April 2020) Broad scientists release COVID-19 best-practices workflows and analysis tools in Terra
- (April 2020) Workflow updates to the COVID-19 workspace: Better viral assembly and phylogenetics with NextStrain
- (April 2020) COVID-19 Integrated Analyses using Single Cell Data
- (June 2020) COVID-19 Genomic Surveillance in the Boston Area - Powered by Terra
- (July 2020) Single-cell transcriptome atlas of COVID-19 in primates arms scientists in the fight against SARS-CoV-2
- (August 2020) COVID-19 viral genomics: Updated public workspace and Boston outbreak preprint in medRxiv
- (August 2020) How SARS-CoV-2 spread across greater Boston during pandemic’s first wave
Read preprints highlighting COVID-19 research in Terra
The following are preprint manuscripts that accompany the COVID-19 workspaces.
- (April 2020) Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells.
- (August 2020) Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events
- Related Terra workspaces: COVID-19_cross_tissue_analysis
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: