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

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Zerbino, Daniel R., Birney, Ewan·2008·Genome Research

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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.

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Authors: Zerbino, D. R., & Birney, E.
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2008-03-18
Volume: 18
Issue: 5
Pages: 821-829
ISSN: 1088-9051 (ISSN-L)
DOI: 10.1101/gr.074492.107
OpenAlex: W2160969485
Cited by: 9,491
References: 3
Type: posted content
Language: en
Open access: bronze

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

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