CloG: A pipeline for closing gaps in a draft assembly using short reads

2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011

Volumn , Issue , 2011, Pages 202-207

  Yang, Xing ^a   Medvin, Daniel ^a   Narasimhan, Giri ^a   Yoder Himes, Deborah ^b   Lory, Stephen ^b  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Assembly; Contigs; Finishing; Gaps; Repeat regions; Seeds; Sequencing

Indexed keywords

BURKHOLDERIA; CONTIGS; GAPS; HYBRID ASSEMBLY; REASSEMBLY; REPEAT REGIONS; SEQUENCING; SOFTWARE PIPELINE;

MEDICAL COMPUTING;

EID: 79953834217     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICCABS.2011.5729881     Document Type: Conference Paper

References (19)

1. Burkholderia dolosa Sequencing Project, Broad Institute of Harvard and MIT. [cited; Available from: http://www.broadinstitute.org/annotation/genome/ burkholderia-dolosa/MultiDownloads.html.
2. Adams, J.U., DNA Sequencing Technologies. Nature Education, 2008. 1(1).
3. Assefa, S., T.M. Keane, T.D. Otto, C. Newbold, and M. Berriman, ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics, 2009. 25(15): p. 1968-9.
4. Goldberg, S.M., et al., A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A, 2006. 103(30): p. 11240-5. (Pubitemid 44156503)
5. Gordon, D., C. Abajian, and P. Green, Consed: a graphical tool for sequence finishing. Genome Res, 1998. 8(3): p. 195-202. (Pubitemid 28177231)
6. Han, C.S. and P. Chain. Finishing Repetitive Regions Automatically with Dupfinisher. in International Conference on Bioinformatics and Computational Biology (BIOCOMP'06). 2006.
7. Hert, D.G., C.P. Fredlake, and A.E. Barron, Advantages and limitations of next-generation sequencing technologies: a comparison of electrophoresis and nonelectrophoresis methods. Electrophoresis, 2008. 29(23): p. 4618-26.
8. Langmead, B., C. Trapnell, M. Pop, and S.L. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 2009. 10(3): p. R25.
9. Lapidus, A.L., Genome Sequence Databases (Overview): Sequencing and Assembly. 2009, Lawrence Berkeley National Laboratory.
10. Metzker, M.L., Sequencing technologies - the next generation. Nat Rev Genet, 2010. 11(1): p. 31-46.
11. Miller, J.R., et al., Aggressive assembly of pyrosequencing reads with mates. Bioinformatics, 2008. 24(24): p. 2818-24.
12. Pop, M., A. Phillippy, A.L. Delcher, and S.L. Salzberg, Comparative genome assembly. Brief Bioinform, 2004. 5(3): p. 237-48.
13. Richter, D.C., S.C. Schuster, and D.H. Huson, OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics, 2007. 23(13): p. 1573-9. (Pubitemid 47244446)
14. Samad, A., E.F. Huff, W. Cai, and D.C. Schwartz, Optical mapping: a novel, single-molecule approach to genomic analysis. Genome Res, 1995. 5(1): p. 1-4.
15. Shendure, J. and H. Ji, Next-generation DNA sequencing. Nat Biotechnol, 2008. 26(10): p. 1135-45.
16. Smit, A.F., The origin of interspersed repeats in the human genome. Curr Opin Genet Dev, 1996. 6(6): p. 743-8. (Pubitemid 27010635)
17. Tsai, I.J., T.D. Otto, and M. Berriman, Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol, 2010. 11(4): p. R41.
18. Zerbino, D.R. and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res, 2008. 18(5): p. 821-9. (Pubitemid 351645072)
19. Zimin, A.V., D.R. Smith, G. Sutton, and J.A. Yorke, Assembly reconciliation. Bioinformatics, 2008. 24(1): p. 42-5.