In an effort to slow the impacts of the 2019 novel coronavirus (COVID-19), the Terra team and our scientific collaborators are working quickly to make data and tools for COVID-19 analysis available in Terra as quickly as possible. We will maintain this article in the support center as a landing page for COVID-19-related public resources as well as the educational materials to help you learn how to use them.
We will maintain this article in the support center as further 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.
- 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
Best-practices for processing COVID-19 genomic data
This COVID-19 workspace, developed by Dr. Danny Park and colleagues at the Broad Institute, contains best-practices workflows for taking sequencer output data (either FASTQ or SRA), assembling viral genomes, and running the results against the Kraken taxonomic classifier.
It also contains COVID-19 sample data from around the world, as well as a Jupyter Notebook meant to walk you through how to read in the output data into the notebook and make QC plots. The COVID-19 data in the workspace will be routinely updated as more data become available, as will the sample analyses in the notebook. If you clone a version of this workspace for your own work, be sure to check back regularly to see if you should clone a fresh version (or copy the latest data/notebook to your older workspace).
We also recommend reading our blog articles about this workspace:
- Broad scientists release COVID-19 best-practices workflows and analysis tools in Terra
- Workflow updates to the COVID-19 workspace: Better viral assembly and phylogenetics with NextStrain
Integrated analyses using single cell data
This second COVID-19 workspace, focuses on the cells and organs in the human body that may be infected by the virus.
The Human Cell Atlas Lung Biological Network, including our colleagues at Broad’s Klarman Cell Observatory (KCO) recently shared a manuscript pre-print describing how they used millions of single-cell RNA-seq profiles from 25 tissues and organs to identify the cells likely to be infected with SARS-CoV-2 throughout the body, and the gene expression programs within those cells that could provide clues to disease mechanisms and therapies. The authors of the study wanted to ensure it was possible for others to build on their work by making all of the necessary data and code publicly available. This workspace contains a set of Jupyter notebooks that will allow researchers to reproduce many of the core analyses in their manuscript. The workspace’s Data section also contains metadata from a variety of organ and tissue samples that are necessary for the analysis (age, sex, or smoking status).
Blog article about this workspace:
We will be linking additional COVID-19 resources and educational materials for using them in Terra as we develop them.