ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Cabanski, Christopher R ^a   Cavin, Keary ^b   Bizon, Chris ^b   Wilkerson, Matthew D ^a   Parker, Joel S ^a,c   Wilhelmsen, Kirk C ^a,b,c   Perou, Charles M ^a,c   Marron, J S ^a   Hayes, D N ^a,c  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b Renaissance Computing Center   (United States)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

Bioconductor; Bioinformatics; Next generation sequencing; Quality score; Recalibration

Indexed keywords

BIOCONDUCTOR; LOGISTIC REGRESSIONS; NEXT-GENERATION SEQUENCING; OPEN SOURCE SOFTWARE; RECALIBRATIONS; SEQUENCING ERRORS; SIGNIFICANT IMPACTS;

BIOINFORMATICS; ERRORS; LOGISTICS;

QUALITY CONTROL;

ARTICLE; CALIBRATION; COMPUTER PROGRAM; GENOME; HIGH THROUGHPUT SEQUENCING; SEQUENCE ALIGNMENT; STANDARD; STATISTICAL MODEL;

CALIBRATION; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LOGISTIC MODELS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84865654577     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-221     Document Type: Article

References (16)

1. Lamlertthon W, Hayward MC, Hayes DN. Emerging technologies for improved stratification of cancer patients: a review of opportunities, challenges, and tools. Cancer J 2011, 17:451-464. 10.1097/PPO.0b013e31823bd1f8, 22157289.
2. Zhang J, Chiodini R, Badr A, Zhang G. The impact of next-generation sequencing on genomics. J Genet Genomics 2011, 38:95-109. 10.1016/j.jgg.2011.02.003, 3076108, 21477781.
3. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, 43:491-498. 10.1038/ng.806, 3083463, 21478889.
4. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. SNP detection for massively parallel whole-genome resequencing. Genome Res 2009, 19:1124-1132. 10.1101/gr.088013.108, 2694485, 19420381.
5. Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 2011, 12:443-451. 10.1038/nrg2986, 21587300.
6. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8:186-194.
7. Li H. Improving SNP Discovery by base alignment quality. Bioinformatics 2011, 27:1157-1158. 10.1093/bioinformatics/btr076, 3072548, 21320865.
8. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
9. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
10. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36:e105. 10.1093/nar/gkn425, 2532726, 18660515.
11. Clark MJ, Homer N, O'Connor BD, Chen Z, Eskin A, Lee H, Merriman B, Nelson SF. U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet 2010, 6:e1000832. 10.1371/journal.pgen.1000832, 2813426, 20126413.
12. Sherry ST, Ward M, Sirotkin K. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res 1999, 9:677-679.
13. Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res 2010, 20:273-280. 10.1101/gr.096388.109, 2813483, 20019143.
14. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol 2011, 29:24-26. 10.1038/nbt.1754, 3346182, 21221095.
15. GATK base quality score recalibration http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration.
16. Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 2010, 38:e178. 10.1093/nar/gkq622, 2952873, 20802226.