De novo assembly of short reads with Velvet
Requires Geneious 7.0+
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, 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.
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.
7.0.3 (25 Sep 2014)
- Now supports RNA sequences
7.0.4 (09 Feb 2016)
- Fixed crash when there are 0 length reads and all other reads are shorter than 46
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18:821-829.