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...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Journal of computational biology Jg. 26; H. 9; S. 948
Hauptverfasser: Bonizzoni, Paola, Della Vedova, Gianluca, Pirola, Yuri, Previtali, Marco, Rizzi, Raffaella
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States 01.09.2019
Schlagworte:
parallel algorithms
Burrows–Wheeler transform
multithreading
longest common prefix array
ISSN:1557-8666, 1557-8666
Online-Zugang:Weitere Angaben
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung: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.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1557-8666
1557-8666
DOI:10.1089/cmb.2018.0230