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

Current Protocols in Bioinformatics

Volumn , Issue SUPPL. 31, 2010, Pages

  Zerbino, Daniel R ^a,b  

^a University of California Santa Cruz   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

de Bruijn Graphs; Genome assembly; Next Generation Sequencing

Indexed keywords

COMPUTER; COMPUTER PROGRAM; DATA ANALYSIS SOFTWARE; INFORMATION PROCESSING; INTERNET PROTOCOL; MEDICAL INFORMATICS; PARAMETER; PRACTICE GUIDELINE; PRIORITY JOURNAL; REVIEW; WEB BROWSER;

BASE SEQUENCE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 77956967295     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi1105s31     Document Type: Review

References (18)

1. Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I.A., Belmonte, M.K., Lander, E..S., Nusbaum, C., and, Jaffe, D.B., 2008. ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res. 18: 810 - 820.
2. Cock, P.J., Fields, C.J., Goto, N., Heuer, M.L., and, Rice, P.M., 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 38: 1767 - 1771.
3. Chaisson, M.J., Brinza, D., and, Pevzner, P.A., 2009. De novo fragment assembly with short mate-paired reads: Does the read length matter Genome Res. 19: 336 - 346.
4. Li, H., Handsaker, B., Wysoker, A., Fennel, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and the 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078 - 2079.
5. Li, R., Zhu, H., and, Wang, J., 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20: 265 - 272.
6. Kurtz, S., Narechania, A., Stein, J., and, Ware D., 2008. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9: 517.
7. Pevzner, P.A., Tang, H., and, Waterman, M.S., 2001. An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. U.S.A. 98: 9748 - 9753. (Pubitemid 32769375)
8. Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J., and, Birol, I., 2009. ABySS: A parallel assembler for short read sequence data. Genome Res. 19: 1117 - 1123.
9. Zerbino, D.R., and, Birney, E., 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18: 821 - 829.
10. Zerbino, D.R., McEwen, G.K., Margulies, E.H., and, Birney, E., 2010. Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS ONE 4: e8407.
11. Zerbino and Birney, 2008. See above. This first publication mainly described the implementation of de Bruijn graphs within Velvet and the error-correction algorithm, TourBus.
12. Zerbino et al., 2010. See above. This follow-up paper describes how Velvet resolves complex repeats using long reads or paired-end read information.
13. http://www.ebi.ac.uk/∼zerbino/velvet Velvet Web site, where code and information on Velvet can be downloaded.
14. http://bioinformatics.net.au/software.shtml VelvetOptimiser by Simon Gladman and Torsten Seeman. This wrapper software scans different parameters of Velvet to produce an optimal assembly, as described in.
15. http://solidsoftwaretools.com/gf/project/denovotools/ Colorspace de novo pipeline by Craig Cummings, Vrunda Sheth, and Dima Brinza. These scripts allow you to do all the appropriate colorspace conversions described in (a registration is required, but the software is free).
16. http://solidsoftwaretools.com/gf/project/corona/ The Corona Lite package can be found on this server.
17. http://sourceforge.net/apps/mediawiki/amos/ AMOS suite by the AMOS Consortium. This suite of tools allows the user to manipulate, convert or analyze AFG assembly files.
18. http://tools.invitrogen.com/content/sfs/manuals/SOLiD-SAGE-SoftwareGuide. pdf Colorspace documentation by Applied Biosystems. This document describes colorspace, and the csfasta format in particular.