Manifold de Bruijn graphs

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8701 LNBI, Issue , 2014, Pages 296-310

  Lin, Yu ^a   Pevzner, Pavel A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTING; BIOINFORMATICS; GENES;

ALGORITHMIC TECHNIQUES; DE BRUIJN; DE BRUIJN GRAPHS; GENOME ASSEMBLY; GRAPH CONSTRUCTION; VARIABLE LENGTH;

ITERATIVE METHODS;

EID: 84958522921     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-662-44753-6_22     Document Type: Conference Paper

References (21)

1. Pevzner, P. A.: l-tuple DNA sequencing: computer analysis. J. Biomol. Struct. Dyn. 7, 63-73 (1989)
2. Idury, R. M., Waterman, M. S.: A new algorithm for DNA sequence assembly. J. Comput. Biol. 2(2), 291-306 (1995)
3. Pevzner, P. A., Tang, H., Waterman, M. S.: An Eulerian path approach to DNA fragment assembly. Proc. Nat'l Acad. Sci. 98(17), 9748 (2001)
4. Zerbino, D. R., Birney, E.: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18(5), 821-829 (2008)
5. Chaisson, M. J., Pevzner, P. A.: Short read fragment assembly of bacterial genomes. Genome Research 18(2), 324-330 (2008)
6. Peng, Y., Leung, H. C. M., Yiu, S. M., Chin, F. Y. L.: IDBA - A practical iterative de bruijn graph de novo assembler. In: Berger, B. (ed.) RECOMB 2010. LNCS, vol. 6044, pp. 426-440. Springer, Heidelberg (2010)
7. Butler, J., MacCallum, I., Kleber, M., et al.: ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Research 18(5), 810-820 (2008)
8. Li, R., Zhu, H., Ruan, J., et al.: De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20(2), 265-272 (2010)
9. Chitsaz, H., Yee-Greenbaum, J. L., Tesler, G., et al.: Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature biotechnology (2011)
10. Bankevich, A., Nurk, S., et al.: Spades: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5), 455-477 (2012)
11. Pevzner, P. A., Tang, H., Tesler, G.: De novo repeat classification and fragment assembly. Genome Research 14(9), 1786-1796 (2004)
12. Böcker, S.: Sequencing from compomers: Using mass spectrometry for DNA denovo sequencing of 200+ nt. In: Benson, G., Page, R. D. M. (eds.) WABI 2003. LNCS (LNBI), vol. 2812, pp. 476-497. Springer, Heidelberg (2003)
13. Pham, S. K., Pevzner, P. A.: DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics 26(20), 2509-2516 (2010)
14. Raphael, B., Zhi, D., Tang, H., Pevzner, P. A.: A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Research 14(11), 2336-2346 (2004)
15. Dean, F. B., Nelson, J. R., Giesler, T. L., Lasken, R. S.: Rapid amplification of plasmid and phage dna using phi29 dna polymerase and multiply-primed rolling circle amplification. Genome Research 11(6), 1095-1099 (2001)
16. Peng, Y., Leung, H., Yiu, S., Chin, F.: IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28(11), 1420-1428 (2012)
17. Gurevich, A., Saveliev, V., Vyahhi, N., Tesler, G.: QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8), 1072-1075 (2013)
18. Magoc, T., Pabinger, S., Canzar, S., et al.: GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics 29(14), 1718-1725 (2013)
19. Compeau, P. E. C., Pevzner, P. A.: Bioinformatics Algorithms: An Active-Learning Approach. Active Learning Publishers (2014)
20. Ilie, L., Smyth, W. F.: Minimum unique substrings and maximum repeats. Fundamenta Informaticae 110(1), 183-195 (2011)
21. Gusfield, D.: Algorithms on strings, trees and sequences: computer science and computational biology. Cambridge University Press (1997)