Population Genomics is a Data Management Problem (TileDB Webinar)
For a summary see the blog post at https://tiledb.com/blog/population-ge.... We were honored to feature Dr. Stephen Kingsmore, President and CEO of Rady Children's Institute for Genomic Medicine, as a guest speaker in our webinar. Special thanks to Helix (helix.com) for their multi-year partnership and immense contributions to our TileDB-VCF offering.
About the presentation
Population genomics is an important and challenging problem plagued by non-scalable domain-specific formats, which make it difficult to efficiently store, access, share and analyze massive amounts of variant-call data at the scale required for gaining meaningful insights. TileDB addresses this challenge with a universal database that stores variant-call data as multi-dimensional arrays that can be updated, governed and analyzed at unprecedented scale and low cost.
In this comprehensive presentation of TileDB’s population genomics solution, TileDB-VCF, you will learn how to:
• Model genomic variants as a 3D sparse array
• Efficiently update variant datasets, solving the N+1 problem
• Ingest huge collections of VCF samples in parallel on TileDB Cloud
• Export to VCF for full compatibility with existing tools
• Share access to TB of variant datasets avoiding file downloads
• Implement scalable genome-wide analyses using serverless compute
• Enable reproducible science and collaboration through code and data sharing
Contents of this video
0:00:00 – Introduction
0:03:39 – The problem in population genomics
0:19:31 – A solution template
0:22:36 – The solution with TileDB
0:32:59 – Dr. Stephen Kingsmore, Rady Children's Institute for Genomic Medicine
0:44:31 – TileDB-VCF basics
1:01:12 – Building scalable genome-wide analyses on TileDB Cloud
1:09:13 – Integrative clinical genomic workflows
1:17:30 – Work in progress
1:21:13 – Q&A
Reproduce the examples on TileDB Cloud
• 1000 Genomes Project High-Coverage Variant Calls data set: https://cloud.tiledb.com/arrays/detai...
• TileDB-VCF basics: https://cloud.tiledb.com/notebooks/de...
• Building scalable genome-wide analyses on TileDB Cloud: https://cloud.tiledb.com/notebooks/de...
• Integrative clinical genomic workflows: https://cloud.tiledb.com/notebooks/de...
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