Using the Velvet de novo assembler for short-read sequencing technologies
- PMID: 20836074
- PMCID: PMC2952100
- DOI: 10.1002/0471250953.bi1105s31
Using the Velvet de novo assembler for short-read sequencing technologies
Abstract
The Velvet de novo assembler was designed to build contigs and eventually scaffolds from short-read sequencing data. This protocol describes how to use Velvet, interpret its output, and tune its parameters for optimal results. It also covers practical issues such as configuration, using the VelvetOptimiser routine, and processing colorspace data.
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References
Literature
4. Key References
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Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–829. This first publication mainly described the implementation of de Bruijn graphs within Velvet and the error correction algorithm,
TourBus .
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Zerbino DR, McEwen GK, Margulies EH, Birney E. Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler. PLoS ONE. 2010;4(12):e8407. This follow-up paper describes how Velvet resolves complex repeats using long reads or paired-end read information.
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5. Internet Resources
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- Velvet website Code and information on Velvet can be downloaded at: www.ebi.ac.uk/~zerbino/velvet.
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- Gladman Simon, Seeman Torsten. VelvetOptimiser. This wrapper software scans different parameters of Velvet to produce an optimal assembly, as described in Support Protocol 2. http://bioinformatics.net.au/software.shtml.
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- Cummings Craig, Sheth Vrunda, Brinza Dima. Colorspace de novo pipeline. These scripts allow you to do all the appropriate colorspace conversions described in Support Protocol 3 (a registration is required, but the software is free): http://solidsoftwaretools.com/gf/project/denovotools/ The Coronal Lite package can also be found on that server: http://solidsoftwaretools.com/gf/project/corona/
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- the AMOS Consortium AMOS suite. This suite of tools allows the user to manipulate, convert or analyze AFG assembly files: http://sourceforge.net/apps/mediawiki/amos/
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- Colorspace documentation. Applied Biosystems This documents describes colorspace, and the csfasta format in particular: http://tools.invitrogen.com/content/sfs/manuals/SOLiD_SAGE_SoftwareGuide....
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