Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

@inproceedings{Zerbino2009PebbleAR,
  title={Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler},
  author={Daniel R. Zerbino and Gayle McEwen and Elliott H. Margulies and Ewan Birney},
  booktitle={PloS one},
  year={2009}
}
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… CONTINUE READING
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