Getting Started on AnVIL
September 15, 2025
About this Book
This book is part of a series of books for the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) of the National Human Genome Research Institute (NHGRI). Here, we present opinionated step-by-step guides for setting up accounts focused on three personas: PIs, Analysts, and Consortia.
Skills Level
Please choose the closest matching persona from the lefthand menu.
Genetics
Novice: no genetics knowledge needed
Programming skills
Novice: no programming experience needed
How to Use This Book
This book is not intended to be read through sequentially, rather, it is a collection of guides that you can reference based on your needs. It is divided into two major sections:
Account Setup
Step-by-step instructions for new AnVIL users to set up their accounts and start using the AnVIL platform. We have included recommendations for configuring your accounts based on several common use cases:
- PIs and Lab Managers: managing a team of researchers working on AnVIL
- Data Analysts: joining a team working on AnVIL
- Consortia: using AnVIL as part of a research consortium
Working on AnVIL
Examples and walkthroughs of common tasks on the AnVIL platform:
- Workspaces: how to create and clone research spaces on AnVIL
- Tools: how to run common tools including Jupyter Notebooks, Galaxy, and RStudio
- Data: how to find and access AnVIL datasets, as well as upload and manage your own data
- Workflows: how to find and run existing automated data processing pipelines, and how to customize and share your own
Activate scroll_highlight Feature
Note that some sections of this book cover steps in a lot of detail. When navigating the table of contents, you can click subsection (e.g., 2.1, 4.3) headers a second time to expand the table of contents and enable the scroll_highlight feature. This can help you follow the separate steps within more clearly.
