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

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

SUBMITTER: Zerbino DR 

PROVIDER: S-EPMC2793427 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature