Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array

Indexing huge collections of strings, such as those produced by the widespread sequencing technologies, heavily relies on multistring generalizations of the Burrows-Wheeler transform (BWT) and the longest common prefix (LCP) array, since solving efficiently both problems are essential ingredients of...

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Bibliographic Details
Published in:Journal of computational biology Vol. 26; no. 9; p. 948
Main Authors: Bonizzoni, Paola, Della Vedova, Gianluca, Pirola, Yuri, Previtali, Marco, Rizzi, Raffaella
Format: Journal Article
Language:English
Published: United States 01.09.2019
Subjects:
parallel algorithms
Burrows–Wheeler transform
multithreading
longest common prefix array
ISSN:1557-8666, 1557-8666
Online Access:Get more information
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Summary:Indexing huge collections of strings, such as those produced by the widespread sequencing technologies, heavily relies on multistring generalizations of the Burrows-Wheeler transform (BWT) and the longest common prefix (LCP) array, since solving efficiently both problems are essential ingredients of several algorithms on a collection of strings, such as those for genome assembly. In this article, we explore a multithread computational strategy for building the BWT and LCP array. Our algorithm applies a divide and conquer approach that leads to parallel computation of multistring BWT and LCP array. Indexing huge collections of strings, such as those produced by the widespread sequencing technologies, heavily relies on multistring generalizations of the Burrows-Wheeler transform (BWT) and the longest common prefix (LCP) array, since solving efficiently both problems are essential ingredients of several algorithms on a collection of strings, such as those for genome assembly. In this article, we explore a multithread computational strategy for building the BWT and LCP array. Our algorithm applies a divide and conquer approach that leads to parallel computation of multistring BWT and LCP array.
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ISSN:1557-8666
1557-8666
DOI:10.1089/cmb.2018.0230