Efficient indexed alignment of contigs to optical maps

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

Volumn 8701 LNBI, Issue , 2014, Pages 68-81

  Muggli, Martin D ^a   Puglisi, Simon J ^b   Boucher, Christina ^a  

^a Colorado State University   (United States)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; MAPPING; SCAFFOLDS;

CONTIGS; CPU TIME; DATA GENERATION; IN-SILICO; LABORATORY TECHNIQUES; OPTICAL MAPPING; OPTICAL MAPS;

GENES;

EID: 84958538672     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-662-44753-6_6     Document Type: Conference Paper

References (36)

1. Alkan, C., Sajjadian, S., Eichler, E.: Limitations of next-generation genome sequence assembly. Nat. Methods 8(1), 61-65 (2010)
2. Anantharaman, T., Mishra, B.: A probabilistic analysis of false positives in optical map alignment and validation. In: Proc. of WABI, pp. 27-40 (2001)
3. Antoniotti, M., Anantharaman, T., Paxia, S., Mishra, B.: Genomics via optical mapping iv: sequence validation via optical map matching. Technical report, New York University (2001)
4. Aston, C., Schwartz, D.: Optical mapping in genomic analysis. John Wiley and Sons, Ltd. (2006)
5. Bankevich, A., et al.: others. SPAdes: a new Genome assembly algorithm and its applications to single-cell sequencing. J. Comp. Biol. 19(5), 455-477 (2012)
6. Bradnam, K. R., et al.: Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2(1), 1-31 (2013)
7. Burrows, M., Wheeler, D.: A block sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation, Palo Alto, California (1994)
8. Chamala, S., et al.: Assembly and validation of the genome of the nonmodel basal angiosperm amborella. Science 342(6165), 1516-1517 (2013)
9. Church, D. M., et al.: Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biology 7(5), e1000112+ (2009)
10. Dimalanta, et al.: A microfluidic system for large dna molecule arrays. Anal. Chem. 76(18), 5293-5301 (2004)
11. Dong, Y., et al.: Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (capra hircus). Nat. Biotechnol. 31(2), 136-141 (2013)
12. Ferragina, P., Manzini, G.: Indexing compressed text. J. ACM 52(4), 552-581 (2005)
13. Gagie, T., Navarro, G., Puglisi, S. J.: New algorithms on wavelet trees and applications to information retrieval. Theor. Comput Sci. 426-427, 25-41 (2012)
14. Gog, S., Petri, M.: Optimized succinct data structures for massive data. Software Pract. Expr. (to appear)
15. Gurevich, A., Saveliev, V., Vyahhi, N., Tesler, G.: QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8), 1072-1075 (2013)
16. Howard, J. T., et al.: De Novo high-coverage sequencing and annotated assemblies of the budgerigar genome (2013)
17. Kawahara, Y., et al.: Improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data. Rice 6(4), 1-10 (2013)
18. Kent, J.: BLAT-The BLAST-Like Alignment Tool. Genome Res. 12(4), 656-664 (2002)
19. Lin, H., et al.: AGORA: Assembly Guided by Optical Restriction Alignment. BMC Bioinformatics 12, 189 (2012)
20. Manber, U., Myers, G. W.: Suffix arrays: A new method for on-line string searches. SIAM J. Sci. Comput. 22(5), 935-948 (1993)
21. Miller, J. R., et al.: Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24, 2818-2824 (2008)
22. Nagarajan, N., Read, T. D., Pop, M.: Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics 24(10), 1229-1235 (2008)
23. Neely, R. K., Deen, J., Hofkens, J.: Optical mapping of DNA: single-molecule-based methods for mapping genome. Biopolymers 95(5), 298-311 (2011)
24. Reslewic, S., et al.: Whole-genome shotgun optical mapping of rhodospirillum rubrum. Appl. Environ. Microbiol. 71(9), 5511-5522 (2005)
25. Ronen, R., Boucher, C., Chitsaz, H., Pevzner, P.: SEQuel: Improving the Accuracy of Genome Assemblies. Bioinformatics 28(12), i188-i196 (2012)
26. Salzberg, S.: Beware of mis-assembled genomes. Bioinformatics 21(24), 4320-4321 (2005)
27. Sirén, J., Välimäki, N., Mäkinen, V.: Indexing graphs for path queries with applications in genome research. IEEE/ACM Trans. Comput. Biol. Bioinform. (to appear, 2014)
28. Teague, B., et al.: High-resolution human genome structure by single-molecule analysis. Proc. Natl. Acad. Sci. 107(24), 10848-10853 (2010)
29. Thorvaldsdòttir, H., Robinson, J. T., Mesirov, J. P.: Integrative Genomics Viewer (IGV): High-performance Genomics Data Visualization and Exploration. Brief. Bioinform. 14(2), 178-192 (2013)
30. Valouev, A., et al.: Alignment of optical maps. J. Comp. Biol. 13(2), 442-462 (2006)
31. VanSteenHouse, H. personal communication (2013)
32. Zhou, S., et al.: A whole-genome shotgun optical map of yersinia pestis strain KIM. Appl. Environ. Microbiol. 68(12), 6321-6331 (2002)
33. Zhou, S., et al.: Shotgun optical mapping of the entire leishmania major Friedlin genome. Mol. Biochem. Parasitol. 138(1), 97-106 (2004)
34. Zhou, S., et al.: A single molecule scaffold for the maize genome. PLoS Genet. 5(11), e1000711 (2009)
35. Zhou, S., et al.: Validation of rice genome sequence by optical mapping. BMC Genomics 8(1), 278 (2007)
36. Zimin, A., et al.: Sequencing and assembly of the 22-gb loblolly pine genome. Genetics 196(3), 875-890 (2014)