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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Vydáno v:Journal of computational biology Ročník 26; číslo 9; s. 948
Hlavní autoři: Bonizzoni, Paola, Della Vedova, Gianluca, Pirola, Yuri, Previtali, Marco, Rizzi, Raffaella
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 01.09.2019
Témata:
parallel algorithms
Burrows–Wheeler transform
multithreading
longest common prefix array
ISSN:1557-8666, 1557-8666
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Shrnutí: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.
Bibliografie:ObjectType-Article-1
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ISSN:1557-8666
1557-8666
DOI:10.1089/cmb.2018.0230