NHGRI Analysis Visualization and Informatics Lab-space
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Secure, cost-effective genomic analysis at scale.
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A complete reference genome improves analysis of human genetic variation

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Using the AnVIL, researchers find the T2T-CHM13 reference genome universally improves the analysis of human genetic variation.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

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AnVIL inverts the traditional model of genomic analysis, eliminating data movement and providing scalable, shared computing resources.

AnVIL Shorts: How can AnVIL help my research?

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Our short video series shows how AnVIL improves collaborative science for different researcher roles.

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

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Using the AnVIL, researchers investigate the effect of superspreading events in the Boston area.

The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols

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Dockstore is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows.

Orchestrating single-cell analysis with Bioconductor

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The AnVIL hosts a detailed book of single-cell methods and analysis techniques.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

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AnVIL has access to full Galaxy capabilities, a computational workbench used by thousands of scientists to analyze biomedical data.
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Terra

Collaborate in Terra, AnVIL's secure, scalable, cloud compute environment.

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Gen3

Manage, harmonize, and share large datasets.

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Dockstore

Create and share Docker-based workflows.

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NCPI

Interoperate with other NIH data commons.

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Bioconductor

Analyze genomic data in the R statistical language.

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Galaxy

Run batch analysis workflows and interactive visualizations.

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Jupyter

Run interactive analysis with python or R.

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Seqr

Identify disease-causing variants.

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Access diverse, open and controlled access, cloud-hosted datasets

500+ Cohorts
4+ Petabytes
600+ thousandParticipants

CMG

Centers for Mendelian Genetics
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CCDG

Centers for Common Disease Genomics
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GTEx

The Genotype-Tissue Expression Project
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1000G

The 1000 Genomes Project
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eMERGE

Electronic and MEdical Records and Genomics Project
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PAGE

Population Architecture Using Genomics and Epidemiology
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HPRC

Human Pangenome Reference Consortium
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T2T

Telomere-to-Telomere
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Convergent Neuro

Convergent Neuro Consortium
Datasets
Consortia RoadmapExplore DatasetsContribute Data

Create, share, and reuse reproducible analysis workspaces

Workspaces aggregate data and analysis methods. Start quickly from an existing workspace and customize it to your needs.

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GATK - Best practices for somatic CNV discovery

A somatic copy number variation workflow, representing the Variant Discovery portion of the Somatic CNV Discovery pipeline.
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GATK - Best Practices for Germline SNPs & Indels

A fully reproducible example of Processing For Variant Discovery, HaplotypeCallerGVCF, and Joint Discovery workflows.
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Hail GWAS PIPELINE

A basic tutorial for using Hail, a python-based package for working with genomic data.
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inferCNV Tumor Single-Cell RNA-Seq Analysis Pipeline

Compare RNA from tumor samples with corresponding “normal” samples to identify evidence for copy number variations in tumors.
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Optimus Pipeline

The Optimus pipeline processes 3-prime single-cell transcriptome data from the 10X Genomics v2 (and v3) assay.
Explore Workspaces

Collaborate in a secure, cost-effective, scalable, cloud-based environment

Reduce compute and storage costs, reduce security and compliance overhead, scale to meet your needs.

Reduce Data Transfer Fees

There is no charge for data transferred from cloud storage to cloud compute within the same region.

Reduce Data Storage Costs

AnVIL hosted datasets are stored free of charge to researchers.

Collaborate Securely

Securely work with controlled-access data in Terra, AnVIL's FedRAMP Moderate compliant analysis platform.

Publish Reproducible Results

Share analyses and workspaces to demonstrate replicable and repeatable science.

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Updates, training events, and workshops

Find out about AnVIL tool and platform updates, training opportunities, and conferences.

News

Scheduled Downtime for AnVIL Data Housing WorkspacesAug 10, 2022
Announcing the AnVIL Cloud Credits Continued Program (AC3) AwardeesMay 03, 2022
Announcing the AnVIL Cloud Credits Continued Program (AC3)Nov 22, 2021
Announcing the AnVIL Cloud Credits Program (AC2) AwardeesJun 03, 2021
AnVIL Hosts Release 1 of the Human Pangenome Reference Consortium DataMar 11, 2021
Announcing Seqr Availability in AnVILMar 10, 2021
NHGRI AnVIL Cloud Platform Now Supports Free Export of GTEx DataOct 20, 2020
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Events

27Apr2023AnVIL Demos: Using the Human Pangenome on AnVIL
09May2023CSHL Biology of Genomes 2023
18May2023AnVIL Demos: WARP Pipelines in AnVIL/Terra
22Jun2023AnVIL Demos: How to use data across multiple AnVIL workspaces
10Jul2023Galaxy Community Conference 2023
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Recent Publications

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Jasmine and Iris: population-scale structural variant comparison and analysis - Melanie Kirsche, Gautam Prabhu, Rachel Sherman, Bohan Ni, Alexis Battle, et al. (2023). Nature Methods. https://doi.org/10.1038/s41592-022-01753-3.
Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing - Sam Kovaka, Shujun Ou, Katharine M. Jenike, Michael C. Schatz, et al. (2023). Nature Methods. https://doi.org/10.1038/s41592-022-01716-8.
The complete sequence of a human Y chromosome - Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, et al. (2022). https://www.biorxiv.org/. https://doi.org/10.1101/2022.12.01.518724.
The Human Pangenome Project: a global resource to map genomic diversity - Ting Wang, Lucinda Antonacci-Fulton, Kerstin Howe, Heather A. Lawson, Julian K. Lucas, et al. (2022). Nature. https://doi.org/10.1038/s41586-022-04601-8.
Diversifying the genomic data science research community - The Genomic Data Science Community Network, et al. (2022). Genome Research. https://doi.org/10.1101/gr.276496.121.
seqr: A web‐based analysis and collaboration tool for rare disease genomics - Lynn S. Pais, Hana Snow, Ben Weisburd, Shifa Zhang, Samantha M. Baxter, et al. (2022). Human Mutation. https://doi.org/10.1002/humu.24366.
A complete reference genome improves analysis of human genetic variation - Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, et al. (2022). Science. https://doi.org/10.1126/science.abl3533.
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) - Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, et al. (2022). Cell Genomics. https://doi.org/10.1101/2021.04.22.436044.
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events - Jacob E. Lemieux, Katherine J. Siddle, Bennett M. Shaw, Christine Loreth, Stephen F. Schaffner, et al. (2021). Science. https://doi.org/10.1126/science.abe3261.
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols - Denis Yuen, Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, et al. (2021). Nucleic Acids Research. https://doi.org/10.1093/nar/gkab346.
Orchestrating single-cell analysis with Bioconductor - Robert A. Amezquita, Aaron T. L. Lun, Etienne Becht, Vince J. Carey, Lindsay N. Carpp, et al. (2020). Nature Methods. https://doi.org/10.1038/s41592-019-0654-x.
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update - Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, et al. (2020). Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa434.
Parliament2: Accurate structural variant calling at scale - Samantha Zarate, Andrew Carroll, Medhat Mahmoud, Olga Krasheninina, Goo Jun, et al. (2020). GigaScience. https://doi.org/10.1093/gigascience/giaa145.
Centers for Mendelian Genomics: A decade of facilitating gene discovery - Samantha M. Baxter, Jennifer E. Posey, Nicole J. Lake, Nara Sobreira, Jessica X. Chong, et al. (2021). medRxiv. https://doi.org/10.1101/2021.08.24.21261656.
The Need for a Human Pangenome Reference Sequence - Karen H. Miga, Ting Wang, et al. (2021). Annual Review of Genomics and Human Genetics. https://doi.org/10.1146/annurev-genom-120120-081921.
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis - Kristoffer Sahlin, Paul Medvedev, et al. (2021). Nature Communications. https://doi.org/10.1038/s41467-020-20340-8.
Cloud bursting galaxy: federated identity and access management - Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks, et al. (2020). Bioinformatics. https://doi.org/10.1093/bioinformatics/btz472.
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