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

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


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.

MeSH terms

  • Base Sequence
  • Sequence Analysis, DNA / methods*
  • Software*