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. 2010 Sep:Chapter 11:Unit 11.5.
doi: 10.1002/0471250953.bi1105s31.

Using the Velvet de novo assembler for short-read sequencing technologies

Daniel R Zerbino  1
Affiliations

Using the Velvet de novo assembler for short-read sequencing technologies

Daniel R Zerbino. Curr Protoc Bioinformatics. 2010 Sep.

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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Figures

Figure 1
Figure 1. Schematic representation of the coverage distribution
The solid curve represents the expected k-mers coverage distribution in an idealized sequencing project of a repeat-free genome, i.e. a Poisson distribution. The dashed curve schematically represents the k-mer coverage distribution in a typical experimental situation. The variance of the main peak is increased, and new peaks are created by erroneous k-mers (left-most peak with minimal coverage) and repeated coverage (smaller peaks on the right). Finally, the dotted curve schematically represents the distribution after a successful assembly. The width of the peaks is tightened because of the averaging over whole contigs.
See this image and copyright information in PMC

References

Literature

    1. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Research. 2008;18:810–820. - PMC - PubMed
    1. Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. N.A.R. 2010;38(6):1767–1771. - PMC - PubMed
    1. Chaisson MJ, Brinza D, Pevzner PA. De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Research. 2009;19:336–346. - PMC - PubMed
    1. Li H, Handsaker B, Wysoker A, Fennel T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, the 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. - PMC - PubMed
    1. Li R, Zhu H, Wang J. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. In press. - PMC - PubMed

4. Key References

    1. 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.

    1. 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.

5. Internet Resources

    1. Velvet website Code and information on Velvet can be downloaded at: www.ebi.ac.uk/~zerbino/velvet.
    1. 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.
    1. 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/
    1. 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/
    1. 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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