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Curr Protoc Bioinformatics. 2010 Sep;Chapter 11:Unit 11.5. doi: 10.1002/0471250953.bi1105s31.

Using the Velvet de novo assembler for short-read sequencing technologies.

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  • 1Center for Biomolecular Science and Engineering, Santa Cruz, California, USA.

Abstract

The Velvet de novo assembler was designed to build contigs and eventually scaffolds from short-read sequencing data. This protocol describes how to use Velvet, interpret its output, and tune its parameters for optimal results. It also covers practical issues such as configuration, using the VelvetOptimiser routine, and processing colorspace data.

PMID:
20836074
PMCID:
PMC2952100
DOI:
10.1002/0471250953.bi1105s31
[PubMed - indexed for MEDLINE]
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