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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

Journal Title

Journal ISSN

Volume Title

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.

Description

2018 Fall.
Includes bibliographical references.

Rights Access

Subject

FM-Index
genomics
de Bruijn graph
succinct data structures
genome assembly

Citation

Associated Publications