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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; GAGE; SSAKE; SHARCGS; ARACHNE; BLAT; BWA; Soap; IDBA; MEGAHIT; IDBA-UD; SHRiMP; QUAST; IDBA-Tran; Mauve; BESST; KMC
Referenced in: 25 Publications
all top 5

Referenced by 80 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 Lima, Lucélia
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

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