UNIT 11.5 Using the Velvet de novo Assembler for Short-Read Sequencing Technologies

  1. Daniel R. Zerbino1,2

Published Online: 1 SEP 2010

DOI: 10.1002/0471250953.bi1105s31

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Zerbino, D. R. 2010. Using the Velvet de novo Assembler for Short-Read Sequencing Technologies. Current Protocols in Bioinformatics. 31:11.5:11.5.1–11.5.12.

Author Information

  1. 1

    Center for Biomolecular Science and Engineering, Santa Cruz, California

  2. 2

    EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, United Kingdom

Publication History

  1. Published Online: 1 SEP 2010
  2. Published Print: SEP 2010


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. Curr. Protoc. Bioinform. 31:11.5.1-11.5.12. © 2010 by John Wiley & Sons, Inc.


  • Genome assembly;
  • Next-Generation Sequencing;
  • de Bruijn Graphs