In this paper we present an efficient external memory algorithm to compute the string graph from a collection of reads, which is a fundamental data representation used for sequence assembly. Our algorithm builds upon some recent results on lightweight Burrows-Wheeler Transform (BWT) and Longest Common Prefix (LCP) construction providing, as a by-product, an efficient procedure to extend intervals of the BWT that could be of independent interest. We have implemented our algorithm and compared its efficiency against SGA-the most advanced assembly string graph construction program
Bonizzoni, P., DELLA VEDOVA, G., Pirola, Y., Previtali, M., Rizzi, R. (2014). Constructing String Graphs in External Memory. In Algorithms in Bioinformatics (pp.311-325). Springer [10.1007/978-3-662-44753-6_23].
Constructing String Graphs in External Memory
BONIZZONI, PAOLA;DELLA VEDOVA, GIANLUCA;PIROLA, YURI;PREVITALI, MARCO;RIZZI, RAFFAELLA
2014
Abstract
In this paper we present an efficient external memory algorithm to compute the string graph from a collection of reads, which is a fundamental data representation used for sequence assembly. Our algorithm builds upon some recent results on lightweight Burrows-Wheeler Transform (BWT) and Longest Common Prefix (LCP) construction providing, as a by-product, an efficient procedure to extend intervals of the BWT that could be of independent interest. We have implemented our algorithm and compared its efficiency against SGA-the most advanced assembly string graph construction program
| File | Dimensione | Formato | |
|---|---|---|---|
|
conf-paper-14-wabi.pdf
Solo gestori archivio
Descrizione: Articolo principale
Dimensione
286.96 kB
Formato
Adobe PDF
|
286.96 kB | Adobe PDF | Visualizza/Apri Richiedi una copia |
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
