Journal
GENOME RESEARCH
Volume 18, Issue 5, Pages 821-829Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.074492.107
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Funding
- Medical Research Council [G0300762] Funding Source: researchfish
- MRC [G0300762] Funding Source: UKRI
- Medical Research Council [G0300762] Funding Source: Medline
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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 similar to 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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