Velvet
| swMATH ID: | 17026 |
| Software Authors: | Zerbino, D. R.; Birney, E. |
| Description: | Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. 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 approximately 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. |
| Homepage: | https://www.ncbi.nlm.nih.gov/pubmed/18349386 |
| Related Software: | ALLPATHS; ABySS; SPAdes; SOAPdenovo; SHARCGS; SSAKE; ARACHNE; GAGE; QUAST; BLAT; IDBA; MEGAHIT; IDBA-UD; SHRiMP; Soap; BWA; BLASTZ; DARRC; KMC; MUMMER |
| Cited in: | 27 Documents |
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Cited by 81 Authors
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