Velvet swMATH ID: 17026 Software Authors: D. R. Zerbino, E. Birney 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; ARACHNE; SHARCGS; GAGE; SSAKE; BLAT; SHRiMP; BWA; Soap; IDBA; MEGAHIT; IDBA-UD; QUAST; QSRA; Rfam; DARRC; IDBA-Tran Cited in: 25 Publications all top 5 Cited by 79 Authors 2 Błażewicz, Jacek 2 Frohmberg, Wojciech 2 Iliopoulos, Costas S. 2 Kasprzak, Marta 2 Kierzynka, Michal 2 Kundu, Ritu 2 Mohamed, Manal 2 Świercz, Aleksandra 2 Vayani, Fatima 2 Wojciechowski, Paweł T. 1 Acuña, Vicente 1 Aleksandrov, A. V. 1 Alipanahi, Bahar 1 Aluru, Srinivas 1 Aransay, Ana M. 1 Boucher, Christina 1 Branković, Ljiljana 1 Chateau, Annie 1 Chikhi, Rayan 1 Davot, Tom 1 Eizenga, Jordan M. 1 Fernández-Anaya, Guillermo 1 Gibney, Daniel 1 Giroudeau, Rodolphe 1 Grossi, Roberto 1 Hackenberg, Michael 1 Italiano, Giuseppe Francesco 1 Jean, Géraldine 1 Kamal, Md. Sarwar 1 Kazakov, S. V. 1 Keith, Jonathan M. 1 Kota, Karthik 1 Krishnamoorty, Sriram 1 Kulkarni, Milind Narayanrao 1 Ladra, Susana 1 Lee, Richard Chia-Tung 1 Liu, Wenli 1 Liu, Yongchao 1 Lu, Chin Lung 1 Mäkinen, Veli 1 Mallén-Fullerton, Guillermo M. 1 Medvedev, Paul 1 Mitreva, Makedonka 1 Muggli, Martin D. 1 Nimmy, Sonia Farhana 1 Paten, Benedict J. 1 Pellegrina, Leonardo 1 Pissis, Solon P. 1 Pizzi, Cinzia 1 Puglisi, Simon J. 1 Quiroz-Ibarra, J. Emilio 1 Radulescu, Andreea 1 Rizzi, Romeo 1 Rodríguez-Ezpeleta, Naiara 1 Rosen, Yohei M. 1 Rusu, Irena 1 Ryšavý, Petr 1 Sacomoto, Gustavo 1 Sagot, Marie-France 1 Salmela, Leena 1 Schmidt, Bertil 1 Sergushichev, Alexey A. 1 Shalyto, A. A. 1 Shieh, Yi-Kung 1 Shyu, Shyong Jian 1 Sinaimeri, Blerina 1 Tabary, Dorine 1 Thankachan, Sharma V. 1 Tomescu, Alexandru Ioan 1 Tsarev, F. N. 1 Välimäki, Niko 1 Vandin, Fabio 1 Weinstock, George M. 1 Weller, Mathias 1 Wendl, Michael C. 1 Wright, Christopher 1 Wu, Qingbiao 1 Železný, Filip 1 Zurkowski, Piotr all top 5 Cited in 12 Serials 2 Theoretical Computer Science 2 Algorithmica 1 Journal of Mathematical Biology 1 Information and Computation 1 European Journal of Operational Research 1 Foundations of Computing and Decision Sciences 1 Applied Mathematics. Series B (English Edition) 1 Data Mining and Knowledge Discovery 1 International Journal of Biomathematics 1 Algorithms 1 Izvestiya Saratovskogo Universiteta. Novaya Seriya. Seriya Matematika, Mekhanika, Informatika 1 Methods in Molecular Biology all top 5 Cited in 6 Fields 22 Biology and other natural sciences (92-XX) 13 Computer science (68-XX) 12 Combinatorics (05-XX) 2 General and overarching topics; collections (00-XX) 2 Statistics (62-XX) 1 Probability theory and stochastic processes (60-XX) Citations by Year