{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T16:38:09Z","timestamp":1732034289552},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration. We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. We also compare ReQON to other available recalibration tools and show that ReQON is less biased and performs favorably in terms of quality score accuracy.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>ReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. ReQON produces a new BAM file with more accurate quality scores, which can improve the results of downstream analysis, and produces several diagnostic plots showing the effectiveness of the recalibration.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-13-221","type":"journal-article","created":{"date-parts":[[2012,9,4]],"date-time":"2012-09-04T14:45:17Z","timestamp":1346769917000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data"],"prefix":"10.1186","volume":"13","author":[{"given":"Christopher R","family":"Cabanski","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keary","family":"Cavin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Bizon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew D","family":"Wilkerson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joel S","family":"Parker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kirk C","family":"Wilhelmsen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles M","family":"Perou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"JS","family":"Marron","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D Neil","family":"Hayes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,9,4]]},"reference":[{"key":"5373_CR1","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1097\/PPO.0b013e31823bd1f8","volume":"17","author":"W Lamlertthon","year":"2011","unstructured":"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\u2013464. 10.1097\/PPO.0b013e31823bd1f8","journal-title":"Cancer J"},{"key":"5373_CR2","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.jgg.2011.02.003","volume":"38","author":"J Zhang","year":"2011","unstructured":"Zhang J, Chiodini R, Badr A, Zhang G: The impact of next-generation sequencing on genomics. J Genet Genomics 2011, 38: 95\u2013109. 10.1016\/j.jgg.2011.02.003","journal-title":"J Genet Genomics"},{"key":"5373_CR3","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"MA DePristo","year":"2011","unstructured":"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\u2013498. 10.1038\/ng.806","journal-title":"Nat Genet"},{"key":"5373_CR4","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1101\/gr.088013.108","volume":"19","author":"R Li","year":"2009","unstructured":"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\u20131132. 10.1101\/gr.088013.108","journal-title":"Genome Res"},{"key":"5373_CR5","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1038\/nrg2986","volume":"12","author":"R Nielsen","year":"2011","unstructured":"Nielsen R, Paul JS, Albrechtsen A, Song YS: Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 2011, 12: 443\u2013451. 10.1038\/nrg2986","journal-title":"Nat Rev Genet"},{"key":"5373_CR6","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1101\/gr.8.3.186","volume":"8","author":"B Ewing","year":"1998","unstructured":"Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8: 186\u2013194.","journal-title":"Genome Res"},{"key":"5373_CR7","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1093\/bioinformatics\/btr076","volume":"27","author":"H Li","year":"2011","unstructured":"Li H: Improving SNP Discovery by base alignment quality. Bioinformatics 2011, 27: 1157\u20131158. 10.1093\/bioinformatics\/btr076","journal-title":"Bioinformatics"},{"key":"5373_CR8","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"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","journal-title":"Genome Biol"},{"key":"5373_CR9","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"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\u20132079. 10.1093\/bioinformatics\/btp352","journal-title":"Bioinformatics"},{"key":"5373_CR10","doi-asserted-by":"publisher","first-page":"e105","DOI":"10.1093\/nar\/gkn425","volume":"36","author":"JC Dohm","year":"2008","unstructured":"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","journal-title":"Nucleic Acids Res"},{"key":"5373_CR11","doi-asserted-by":"publisher","first-page":"e1000832","DOI":"10.1371\/journal.pgen.1000832","volume":"6","author":"MJ Clark","year":"2010","unstructured":"Clark MJ, Homer N, O\u2019Connor 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","journal-title":"PLoS Genet"},{"key":"5373_CR12","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1101\/gr.9.8.677","volume":"9","author":"ST Sherry","year":"1999","unstructured":"Sherry ST, Ward M, Sirotkin K: dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res 1999, 9: 677\u2013679.","journal-title":"Genome Res"},{"key":"5373_CR13","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1101\/gr.096388.109","volume":"20","author":"Y Shen","year":"2010","unstructured":"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\u2013280. 10.1101\/gr.096388.109","journal-title":"Genome Res"},{"key":"5373_CR14","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson JT, Thorvaldsd\u00f3ttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP: Integrative genomics viewer. Nat Biotechnol 2011, 29: 24\u201326. 10.1038\/nbt.1754","journal-title":"Nat Biotechnol"},{"key":"5373_CR15","unstructured":"GATK base quality score recalibration. http:\/\/www.broadinstitute.org\/gsa\/wiki\/index.php\/Base_quality_score_recalibration"},{"key":"5373_CR16","doi-asserted-by":"publisher","first-page":"e178","DOI":"10.1093\/nar\/gkq622","volume":"38","author":"K Wang","year":"2010","unstructured":"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","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-221.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,28]],"date-time":"2022-01-28T04:42:05Z","timestamp":1643344925000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-221"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,9,4]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5373"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-221","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,9,4]]},"assertion":[{"value":"4 May 2012","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 August 2012","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 September 2012","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"221"}}