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. © 2012 Springer-Verlag.
CITATION STYLE
Chapuis, G., Chikhi, R., & Lavenier, D. (2012). Parallel and memory-efficient reads indexing for genome assembly. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 7204 LNCS, pp. 272–280). https://doi.org/10.1007/978-3-642-31500-8_28
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