Parallel and memory-efficient reads indexing for genome assembly - Archive ouverte HAL Access content directly
Conference Papers Year : 2011

Parallel and memory-efficient reads indexing for genome assembly

Abstract

As genomes, transcriptomes and meta-genomes are being sequenced at a faster pace than ever, there is a pressing need for efficient genome assembly methods. Two practical issues in assembly are heavy memory usage and long execution time during the read indexing phase. In this article, a parallel and memory-efficient method is proposed for reads indexing prior to assembly. Specifically, a hash-based structure that stores a reduced amount of read information is designed. Erroneous entries are filtered on the fly during index construction. A prototype implementation has been designed and applied to actual Illumina short reads. Benchmark evaluation shows that this indexing method requires significantly less memory than those from popular assemblers.
Fichier principal
Vignette du fichier
CP144.pdf (243.29 Ko) Télécharger le fichier
Origin : Files produced by the author(s)
Loading...

Dates and versions

inria-00637536 , version 1 (02-11-2011)

Identifiers

  • HAL Id : inria-00637536 , version 1

Cite

Rayan Chikhi, Guillaume Chapuis, Dominique Lavenier. Parallel and memory-efficient reads indexing for genome assembly. Parallel Bio-Computing 2011, Sep 2011, torun, Poland. ⟨inria-00637536⟩
289 View
368 Download

Share

Gmail Facebook Twitter LinkedIn More