Abstract
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.
Keywords
ContigDe Bruijn sequenceVelvetDe Bruijn graphBiologyk-merSequence assemblyAlgorithmComputer scienceComputational biologyGeneticsCombinatoricsDNA sequencingGenomeMathematicsGene
Affiliated Institutions
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Publication Info
- Year
- 2008
- Type
- article
- Volume
- 18
- Issue
- 5
- Pages
- 821-829
- Citations
- 9539
- Access
- Closed
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Cite This
Daniel R. Zerbino,
Ewan Birney
(2008).
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs.
Genome Research
, 18
(5)
, 821-829.
https://doi.org/10.1101/gr.074492.107
Identifiers
- DOI
- 10.1101/gr.074492.107