Indexing Genomic Databases

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.