Indexing Genomic Databases

Supervisor
Travis Gagie - Diego Portales University - Chile
Date and time
Tuesday, January 15, 2019 at 4:30 PM - Aula verde
Programme Director
External reference
Publication date
January 8, 2019
Department
Computer Science  

Summary

Speaker: Travis Gagie
Diego Portales University and CeBiB
 
Since the first human genomes were sequenced and assembled de novo nearly twenty years ago, hundreds of thousands of others have been sequenced and assembled by variation calling.  That much data is a valuable resource but also a problem for algorithms and data structures designed to handle megabytes or gigabytes but not terabytes or petabytes.  In this talk we take variation calling itself as an example and consider why it should become easier as genomic databases grow, why it has not so far, and why it will soon.  Specifically, we describe a new and scalable version of the FM-index data structure underlying modern DNA aligners.

Contact Person: Zsuzsanna Lipták





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