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Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom

We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25–50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of 8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.

E-mail birney{at}ebi.ac.uk; fax 44-1223-494-468.

[Supplemental material is available online at www.genome.org. The code for Velvet is freely available, under the GNU Public License, at http://www.ebi.ac.uk/~zerbino/velvet.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.074492.107.

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