Incorporating sequence quality data into alignment improves DNA read mapping

Nucleic Acids Research

Volumn 38, Issue 7, 2010, Pages

  Frith, Martin C ^a   Wan, Raymond ^a   Horton, Paul ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; GENE MAPPING; GENETIC ALGORITHM; GENETIC POLYMORPHISM; INSECT GENOME; MATHEMATICAL MODEL; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; PROBABILITY; QUALITY CONTROL; SIMULATION; SYSTEMATIC ERROR; ANIMAL; CHROMOSOME MAP; COMPUTER SIMULATION; DROSOPHILA; GENETICS; METHODOLOGY; SEQUENCE ALIGNMENT; STANDARD;

DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS;

ANIMALS; CHROMOSOME MAPPING; COMPUTER SIMULATION; DROSOPHILA; DROSOPHILA MELANOGASTER; PROBABILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 77954139210     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq010     Document Type: Article

References (17)

1. Cokus, S.J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C.D., Pradhan, S., Nelson, S.F., Pellegrini, M., Jacobsen, S.E. et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 452, 215-219.
2. Li, H., Ruan, J. and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
3. Malde, K. (2008) The effect of sequence quality on sequence alignment. Bioinformatics, 24, 897-900.
4. Na, J.C., Roh, K., Apostolico, A. and Park, K. (2009) Alignment of biological sequences with quality scores. Int. J. Bioinformatics Res. Appl., 5, 97-113.
5. Millar, C.D., Huynen, L., Subramanian, S., Mohandesan, E. and Lambert, D.M. (2008) New developments in ancient genomics. Trends Ecol. Evol., 23, 386-393.
6. Kim, J.H., Waterman, M.S. and Li, L.M. (2007) Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res., 17, 1101-1110.
7. Karlin, S. and Altschul, S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
8. States, D.J., Gish, W. and Altschul, S.F. (1991) Improved sensitivity of nucleic acid database searches using application-specific scoring matrices. Methods Companion to Methods Enzymol., 3, 66-70.
9. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
10. Abouelhoda, M.I., Kurtz, S. and Ohlebusch, E. (2004) Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithms, 2, 53-86.
11. Ma, B., Tromp, J. and Li, M. (2002) PatternHunter: faster and more sensitive homology search. Bioinformatics, 18, 440-445.
12. Burkhardt, S. and Kärkkäinen, J. (2003) Better filtering with gapped q-grams. Fundam. Inform., XXIII, 1001-1018.
13. Kucherov, G., Noé, L. and Roytberg, M. (2005) Multiseed lossless filtration. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 2.
14. Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W. and Haussler, D. (2003) Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA, 100, 11484-11489.
15. Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
16. Qu, W., Hashimoto, S.-I. and Morishita, S. (2009) Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res., 19, 1309-1315.
17. Wijaya, E., Frith, M.C., Suzuki, Y. and Horton, P. (2009) Recount: Expectation maximization based error correction tool for next generation sequencing data. Genome Inform., 23, 189-201