Indexing Genomic Databases

Indexing Genomic Databases
Speaker:  Travis Gagie - Diego Portales University - Chile
  Tuesday, January 15, 2019 at 4:30 PM Aula verde
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

Programme Director

Publication date
January 8, 2019