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PLoS One. 2009 Dec 22;4(12):e8407. doi: 10.1371/journal.pone.0008407.

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.

Author information

1
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. zerbino@ebi.ac.uk

Abstract

BACKGROUND:

Despite the short length of their reads, micro-read sequencing technologies have shown their usefulness for de novo sequencing. However, especially in eukaryotic genomes, complex repeat patterns are an obstacle to large assemblies.

PRINCIPAL FINDINGS:

We present a novel heuristic algorithm, Pebble, which uses paired-end read information to resolve repeats and scaffold contigs to produce large-scale assemblies. In simulations, we can achieve weighted median scaffold lengths (N50) of above 1 Mbp in Bacteria and above 100 kbp in more complex organisms. Using real datasets we obtained a 96 kbp N50 in Pseudomonas syringae and a unique 147 kbp scaffold of a ferret BAC clone. We also present an efficient algorithm called Rock Band for the resolution of repeats in the case of mixed length assemblies, where different sequencing platforms are combined to obtain a cost-effective assembly.

CONCLUSIONS:

These algorithms extend the utility of short read only assemblies into large complex genomes. They have been implemented and made available within the open-source Velvet short-read de novo assembler.

PMID:
20027311
PMCID:
PMC2793427
DOI:
10.1371/journal.pone.0008407
[Indexed for MEDLINE]
Free PMC Article

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