Quality scores and SNP detection in sequencing-by-synthesis systems

Genome Research

Volumn 18, Issue 5, 2008, Pages 763-770

  Brockman, William ^a,c   Alvarez, Pablo ^a,d   Young, Sarah ^a   Garber, Manuel ^a   Giannoukos, Georgia ^a   Lee, William L ^a   Russ, Carsten ^a   Lander, Eric S ^a,b   Nusbaum, Chad ^a   Jaffe, David B ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c GOOGLE INC   (United States)

^d Akamai   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; AMPLICON; ARTICLE; COMPUTER PROGRAM; ERROR; GENE SEQUENCE; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS;

DIPLOIDY; GENOME, HUMAN; HAPLOIDY; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 43149107930     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.070227.107     Document Type: Article

References (10)

1. Altshuler, D., Pollara, V., Cowles, C., Van Etten, W., Baldwin, J., Linton, L., and Lander, E. 2000. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407: 513-516.
2. Applied Biosystems, Inc. 2004. User Bulletin. FAQ, KB Basecaller 1.2. docs.appliedbiosystems.com/pebiodocs/04362968.pdf.
3. Ewing, B. and Green, P. 1998. Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
4. Ewing, B., Hillier, L., Wendl, M., and Green, P. 1998. Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
5. International HapMap Consortium. 2003. The International HapMap Project. Nature 426: 789-796.
6. International SNP Map Working Group. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933.
7. Jaffe, D.B., Butler, J., Gnerre, S., Mauceli, E., Lindblad-Toh, K., Mesirov, J.P., Zody, M.C., and Lander, E.S. 2003. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 13: 91-96.
8. Kuhn, R.M., Karolchik, D., Zweig, A.S., Trumbower, H., Thomas, D.J., Thakkapallayil, A., Sugnet, C.W., Stanke, M., Smith, K.E., Siepel, A., et al. 2007. The UCSC genome browser database: Update 2007. Nucleic Acids Res. 35: D668-D673.
9. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
10. Walther, D., Bartha, G., and Morris, M. 2001. Basecalling with LifeTrace. Genome Res. 11: 875-888.