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Methods and Resources

Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs

¹ European Bioinformatics Institute; ² EBI

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) which is ideal for high coverage, very short read (25-50bp) datasets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50Kb N50 length in simulations of prokaryotic data and 3Kb N50 on simulated mammalian BACs. When applied to real Solexa datasets without readpairs, Velvet generated contigs of around 8Kb in a prokaryote and 2Kb in a mammalian BAC, in close agreement with our simulated results without readpair information. Velvet represents a new approach to assembly which can leverage very short reads in combination with read pairs to produce useful assemblies.

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