De novo assembly of short reads with Velvet

Velvet Plugin

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).

Once installed, run the plugin by selecting your sequencing reads and clicking on Align/Assemble - De Novo Assemble in the toolbar. Velvet is available under the Algorithm drop-down option.


7.0.4 (09 Feb 2016) – Download

Fixed crash when there are 0 length reads and all other reads are shorter than 46

7.0 (02 Sep 2013) – Download

– Upgrade to Velvet 1.2.10

– Implement on desktop Geneious on all 64-bit platforms


Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18:821-829.


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