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Cited by 9,491

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

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

Open access
Zerbino, Daniel R., Birney, Ewan·2008·Genome Research
DOI 10.1101/gr.074492.107
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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.

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Research works printed but not linked: 25

  1. Batzoglou, S. (2005) in Encyclopedia of genomics, proteomics and bioinformatics, Algorithmic challenges in mammalian genome sequence assembly, ed Dunn, M. (John Wiley and Sons, New York) Part 4. · DOI
  2. 10.1101/gr.208902 · DOI · Paper page
  3. 10.1016/j.gde.2006.10.009 · DOI · Paper page
  4. 10.1093/bioinformatics/bti129 · DOI
  5. 10.1093/bioinformatics/bth205 · DOI
  6. 10.1101/gr.6435207 · DOI
  7. Gross, J.L. Yellen, J. (2004) Handbook of graph theory (CRC Press LLC, Boca Raton, FL). · DOI
  8. 10.1101/gr.2264004 · DOI
  9. 10.1101/gr.1390403 · DOI · Paper page
  10. Idury,, 1995, A new algorithm for DNA sequence assembly, J. Comput. Biol., 2, 291, 10.1089/cmb.1995.2.291 · DOI · Paper page
  11. 10.1038/35057062 · DOI · Paper page
  12. 10.1093/bioinformatics/btm451 · DOI
  13. 10.1038/ng.2007.9 · DOI
  14. 10.1126/science.1141319 · DOI · Paper page
  15. 10.1038/nmeth726 · DOI
  16. 10.1016/0888-7543(88)90007-9 · DOI · Paper page
  17. Margulies,, 2005, Genome sequencing in microfabricated high-density picolitre reactors, Nature, 437, 376, 10.1038/nature03959 · DOI · Paper page
  18. 10.1101/gr.3770505 · DOI
  19. 10.1093/bioinformatics/bti1114 · DOI · Paper page
  20. 10.1126/science.287.5461.2196 · DOI · Paper page
  21. 10.1073/pnas.171285098 · DOI · Paper page
  22. Shah, M.K. Lee, H. Rogers, S.A. Touchman, J.W. (2004) Computational Systems Bioinformatics Conference, An exhaustive genome assembly algorithm using k-mers to indirectly perform n-squared comparisons in O(n) (IEEE, New York), pp 740–741.
  23. 10.1186/1471-2105-6-31 · DOI
  24. 10.1371/journal.pone.0000484 · DOI
  25. Warren,, 2007, Assembling millions of short DNA sequences using SSAKE, Bioinformatics, 4, 500, 10.1093/bioinformatics/btl629 · DOI

Cited by

Metadata

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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