Enhancing space and time efficiency of genomics in practice through sophisticated applications of the FM-Index
Date
2018
Authors
Muggli, Martin D., author
McConnell, Ross, advisor
Morley, Paul S., committee member
Chitsaz, Hamid, committee member
Anderson, Charles, committee member
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Abstract
Genomic sequence data has become so easy to get that the computation to process it has become a bottleneck in the advancement of biological science. A data structure known as the FM-Index both compresses data and allows efficient querying, thus can be used to implement more efficient processing methods. In this work we apply advanced formulations of the FM-Index to existing problems and show our methods exceed the performance of competing tools.
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Rights Access
Subject
FM-Index
genomics
de Bruijn graph
succinct data structures
genome assembly