Velvet

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.


References in zbMATH (referenced in 13 articles )

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  1. Blazewicz, Jacek; Kasprzak, Marta; Kierzynka, Michal; Frohmberg, Wojciech; Swiercz, Aleksandra; Wojciechowski, Pawel; Zurkowski, Piotr: Graph algorithms for DNA sequencing -- origins, current models and the future (2018)
  2. Eugene Goltsman, Isaac Ho, Daniel Rokhsar: Meraculous-2D: Haplotype-sensitive Assembly of Highly Heterozygous genomes (2017) arXiv
  3. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  4. Rosen, Yohei; Eizenga, Jordan; Paten, Benedict: Describing the local structure of sequence graphs (2017)
  5. Brankovic, Ljiljana; Iliopoulos, Costas S.; Kundu, Ritu; Mohamed, Manal; Pissis, Solon P.; Vayani, Fatima: Linear-time superbubble identification algorithm for genome assembly (2016)
  6. Iliopoulos, Costas S.; Kundu, Ritu; Mohamed, Manal; Vayani, Fatima: Popping superbubbles and discovering clumps: recent developments in biological sequence analysis (2016)
  7. Tomescu, Alexandru I.; Medvedev, Paul: Safe and complete contig assembly via omnitigs (2016)
  8. Nimmy, Sonia Farhana; Kamal, M.S.: Next generation sequencing under de novo genome assembly (2015)
  9. Blazewicz, Jacek; Frohmberg, Wojciech; Gawron, Piotr; Kasprzak, Marta; Kierzynka, Michal; Swiercz, Aleksandra; Wojciechowski, Pawel: DNA sequence assembly involving an acyclic graph model (2013)
  10. Sergushichev, A.A.; Aleksandrov, A.V.; Kazakov, S.V.; Tsarev, F.N.; Shalyto, A.A.: Combining de Bruijn graphs, overlap graphs and microassembly for \itde novo genome assembly (2013)
  11. Wendl, Michael C.; Kota, Karthik; Weinstock, George M.; Mitreva, Makedonka: Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens’ theorem (2013)
  12. Välimäki, Niko; Ladra, Susana; Mäkinen, Veli: Approximate all-pairs suffix/prefix overlaps (2012)
  13. Schwartz, David C.; Waterman, Michael S.: New generations: sequencing machines and their computational challenges (2009) ioport