AnVIL
NHGRI Analysis Visualizationand Informatics Lab-space
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Overview

  • What is AnVIL?
  • Data Consortia Roadmap
  • Platform and Data Security
  • Supported by NHGRI
  • Publications
  • Citing AnVIL

Publications

Analyzed on AnVIL

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.
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 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.

AnVIL Platform, Data, Tools and Components

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.
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.
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.
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.
Supported by NHGRICiting AnVIL
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