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A complete reference genome improves analysis of human genetic variation

Paper Workspace

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)

Paper

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

Paper Workspace

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.

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

450+ Cohorts

4+ Petabytes

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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 Roadmap Explore Datasets Contribute 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.

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

17Nov2022AnVIL Office Hours - November 2022

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Recent Publications

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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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Tweets by useAnVIL

A complete reference genome improves 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)

AnVIL Shorts: How can AnVIL help my research?

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

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

Orchestrating single-cell analysis with Bioconductor

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

Terra

Gen3

Dockstore

NCPI

Bioconductor

Galaxy

Jupyter

Seqr

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

CMG

CCDG

GTEx

1000G

eMERGE

PAGE

HPRC

T2T

Convergent Neuro

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.

GATK - Best practices for somatic CNV discovery

GATK - Best Practices for Germline SNPs & Indels

Hail GWAS PIPELINE

inferCNV Tumor Single-Cell RNA-Seq Analysis Pipeline

Optimus Pipeline

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

Reduce Data Storage Costs

Collaborate Securely

Publish Reproducible Results

Updates, training events, and workshops

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

News

Events

Mailing List

Keep up-to-date with the latest AnIVL Platform announcements.

Recent Publications

Join the Conversation