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9 - Burrows–Wheeler indexes

from Part III - Genome-Scale Index Structures

Published online by Cambridge University Press:  28 September 2023

Veli Mäkinen ,
Djamal Belazzougui ,
Fabio Cunial  and
Alexandru I. Tomescu
Veli Mäkinen
Affiliation:
University of Helsinki
Djamal Belazzougui
Affiliation:
Centre de Recherche sur l’Information Scientifique et Technique (CERIST), Algiers
Fabio Cunial
Affiliation:
Broad Institute, Massachusetts
Alexandru I. Tomescu
Affiliation:
University of Helsinki
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Summary

Classical index structures like suffix trees are powerful, but they occupy much more space than the data they are built on. Many space-efficient alternatives exist that occupy space close to the input data. This chapter covers such data structures based on the Burrows–Wheeler transform (BWT). A special emphasis is given to the bidirectional BWT index, which can be used for solving basic genome analysis tasks by simulating suffix tree exploration without any sacrifice in run time. Space-efficient representations of de Bruijn graphs are also covered.

Type
Chapter
Information
Genome-Scale Algorithm Design
Bioinformatics in the Era of High-Throughput Sequencing
 , pp. 174 - 216
Publisher: Cambridge University Press
Print publication year: 2023

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