AnVIL API Library
Interact with AnVIL data, analysis solutions, and workflows via a command line interface.
Access thousands of tools via an intuitive graphical user interface for processing batch analysis with Galaxy Workflows and interactive downstream visualizations.
Dockstore is an open platform used by the GA4GH for sharing Docker-based tools described with the Common Workflow Language (CWL), the Workflow Description Language (WDL), or Nextflow (NFL).
Gen3 is a cloud-based software platform for managing, analyzing, harmonizing, and sharing large datasets. Gen3 is an open source platform for developing data commons.
Interactive analysis with the python or R programming languages; the R environment includes a family of Bioconductor 3.10 packages.
Interactive analysis with your favorite R coding platform.
Terra is an analysis platform that allows users to access data, run analysis tools, and collaborate. Terra is powered by Google Cloud Platform, enabling the user to scale and manage billing of their own projects.
Batch processing of GATK and other workflows.
The AnVIL project's featured workspaces demonstrate common genomic analysis pipelines deployed using data and tools available on AnVIL.
These analyses utilize unrestricted public data along with reproducible workflows, allowing researchers to clone and execute the workspaces as a learning exercise or for adapting to their own research.
This is a fully reproducible example of Processing For Variant Discovery, HaplotypeCallerGVCF, and Joint Discovery workflows based on GATK Best Practices.
This workspace contains an example of the somatic copy number variation workflow, representing the Variant Discovery portion of the Somatic CNV Discovery pipeline.
The Optimus pipeline processes 3-prime single-cell transcriptome data from the 10X Genomics v2 (and v3) assay.
The inferCNV workflow compares RNA from tumor samples with corresponding “normal” samples to identify evidence for copy number variations in tumors.
This workspace serves as a basic tutorial for using Hail, a python-based package containing additional data types and methods for working with genomic data.
Release Road Map
AnVIL is continually integrating new high-value data sets, platform components and tools.
Discover AnVIL Virtually at the Online, Global BCC 2020
The 2020 Bioinformatics Community Conference will now be virtual. AnVIL team members will join and present several virtual training workshops covering how to use Dockstore, Terra, R and Bioconductor to execute reproducible workflows in the cloud.
Finding and Analyzing Data in the Cloud with Gen3, Dockstore, Terra, and Galaxy
This full-day workshop will guide you through a research journey that highlights the capabilities and components of the NHGRI Genomic Data Science Analysis, Visualization and Informatics Lab-space (AnVIL) resource.