High-throughput annotation using VRS requires high-performance tools for sequence retrieval, variant normalisation, and variant identification. In this session, we will describe recent updates to the Biocommons Toolkit for high-throughput sequence retrieval and alignment operations, including a discussion of the use of the LSG Work Stream's refget v2.0 and the draft Sequence Collections specifications for building a federated ecosystem of sequence collections. We will discuss how these updates improve high-throughput, federated VRS annotation of variant collections using the GA4GH VRS-Python Toolkit, and recent changes to VRS-Python to further improve variant representation performance.

This session is targeted at implementers seeking to apply GKS in large-scale genomics applications using open-source community tools.