sEQuel: Improving the accuracy of genome assemblies

Bioinformatics

Volumn 28, Issue 12, 2012, Pages

  Ronen, Roy ^a   Boucher, Christina ^b   Chitsaz, Hamidreza ^c   Pevzner, Pavel ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Wayne State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); DELTAPROTEOBACTERIA; ESCHERICHIA COLI;

ALGORITHM; ARTICLE; BACTERIAL GENOME; BIOLOGY; CONTIG MAPPING; DNA SEQUENCE; ESCHERICHIA COLI; GENETICS; INDEL MUTATION; METHODOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; CONTIG MAPPING; ESCHERICHIA COLI; GENOME, BACTERIAL; INDEL MUTATION; SEQUENCE ANALYSIS, DNA;

EID: 84863519354     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts219     Document Type: Article

References (36)

1. Alkan, S. et al. (2011) Limitations of next-generation genome sequence assembly. Nature Meth., 8, 61-65.
2. Bankevich, A. et al. (2012) SPAdes: a New Genome Assembly Algorithm and its Applications to Single-Cell Sequencing. J. Comp. Bio., 19, 455-477.
3. Bentley, D.R. et al. (2008) Accurate whole genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
4. Butler, J. et al. (2008) ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res., 18, 810-820.
5. Chitsaz, H. et al. (2011) Efficient de novo assembly of single-cell bacterial genomes from short-read datasets. Nature Biotech., 29, 915-921.
6. Compeau, P.E.C. et al. (2011) How to apply de Bruijn graphs to genome assembly. Nature Biotech., 29, 987-991.
7. DePristo, M. et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Gene., 43, 491-498.
8. Donmez, N. and Brudno, M. (2011) Hapsembler: as assembler for highly polymorphic genomes. In Bafna, V. and Cenk, S. (eds.) RECOMB 2011, LNCS, Vol. 6577, Springer, Heidelberg, pp. 38-51.
9. Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using Phred.II. ErrorProbabilities. Genome Res., 8, 186-194.
10. Ewing, B. et al. (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res., 8, 175-185.
11. McKenna, A. et al. (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-303.
12. Hannenhalli, S. et al. (1996) Positional sequencing by hybridization. CABIOS, 12, 19-24.
13. Hirschberg, D.S. (1975) A linear space algorithm for computing maximal common subsequences. Comm. A.C.M., 18, 341-343.
14. Huang, S. et al. (2009) The genome of the cucumber: Cucumis sativus L. Nature Gen., 41, 1275-1281.
15. Idury, R.M. and Waterman, M.S. (1995) A new algorithm for dna sequence assembly. J. Comput. Biol., 2, 291-306.
16. Kececioglu, J. and Yu, J. (2001) Separating Repeats in DNA Sequence Assembly. In RECOMB 2001, ACM, New York, NY, pp. 176-183.
17. Kelley, D.R. et al. (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol., 11, R116.
18. Kent, W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664.
19. Klein, J.D. et al. (2011) LOCAS-a low coverage assembly tool for resequencing projects. PLoS One, 6, e23455.
20. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
21. Li, R. et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311-317.
22. Li, R. et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res., 20, 265-272.
23. Myers, G. (2001) Optimally separating sequences. Genome Inform., 12, 165-174.
24. Medvedev, P. et al. (2001) Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics, 27, i137-i141.
25. Genome 10K Community of Scientists. (2009) Genome 10k: a proposal to obtain whole-genome sequence for 10000 vertebrate species. J. Hered., 100, 659-674.
26. Pevzner, P. and Chaisson, M. (2008) Short read fragment assembly of bacterial genomes. Genome Res., 18, 324-330.
27. Pevzner, P. et al. (2004) De novo repeat classification and fragment assembly. Genome Res., 14, 1786-1796.
28. Pevzner, P.A. et al. (2001) An eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci., 98, 9748-9753.
29. Raghunathan, A. et al. (2005) Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol., 71, 3342-3347.
30. Robinson, G.E. et al. (2011) Creating a buzz about insect genomes. Science, 331, 1386.
31. Rodrigue, S. et al. (2009) Whole genome amplification and de novo assembly of single bacterial cells. PLoS One, 4, e6864.
32. Simpson, J.T. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
33. Tammi, M.T. et al. (2002) Separation of nearly identical repeats in shotgun assemblies using defined nucloetide positions, DNPs. Bioinformatics, 18, pp. 379-388.
34. Wheeler, D.A. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.
35. Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome Res., 18, 821-829.
36. Zhi, D. et al. (2007) Correcting base-assignment errors in repeat regions of shotgun assembly. IEEE/ACM Trans. Comput. Biol. Bioinform., 4, 54-64.