{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:32:08Z","timestamp":1761863528817,"version":"3.37.3"},"reference-count":12,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,2,29]],"date-time":"2016-02-29T00:00:00Z","timestamp":1456704000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,2,29]],"date-time":"2016-02-29T00:00:00Z","timestamp":1456704000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000774","name":"Defense Threat Reduction Agency","doi-asserted-by":"publisher","award":["CB10152"],"award-info":[{"award-number":["CB10152"]}],"id":[{"id":"10.13039\/100000774","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Illumina is the most widely used next generation sequencing technology and produces millions of short reads that contain errors. These sequencing errors constitute a major problem in applications such as <jats:italic>de novo<\/jats:italic> genome assembly, metagenomics analysis and single nucleotide polymorphism discovery.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>In this study, we present ADEPT, a dynamic error detection method, based on the quality scores of each nucleotide and its neighboring nucleotides, together with their positions within the read and compares this to the position-specific quality score distribution of all bases within the sequencing run. This method greatly improves upon other available methods in terms of the true positive rate of error discovery without affecting the false positive rate, particularly within the middle of reads.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>ADEPT is the only tool to date that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution of quality scores for the dataset being analyzed. The result is a method that is less prone to position-dependent under-prediction, which is one of the most prominent issues in error prediction. The outcome is that ADEPT improves upon prior efforts in identifying true errors, primarily within the middle of reads, while reducing the false positive rate.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-0967-z","type":"journal-article","created":{"date-parts":[[2016,2,29]],"date-time":"2016-02-29T13:07:10Z","timestamp":1456751230000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["ADEPT, a dynamic next generation sequencing data error-detection program with trimming"],"prefix":"10.1186","volume":"17","author":[{"given":"Shihai","family":"Feng","sequence":"first","affiliation":[]},{"given":"Chien-Chi","family":"Lo","sequence":"additional","affiliation":[]},{"given":"Po-E","family":"Li","sequence":"additional","affiliation":[]},{"given":"Patrick S. G.","family":"Chain","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,2,29]]},"reference":[{"key":"967_CR1","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.tig.2007.12.007","volume":"24","author":"ER Mardis","year":"2008","unstructured":"Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008;24:133\u201341.","journal-title":"Trends Genet"},{"key":"967_CR2","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/nrg2626","volume":"11","author":"ML Metzker","year":"2010","unstructured":"Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11:31\u201346.","journal-title":"Nat Rev Genet"},{"issue":"16","key":"967_CR3","doi-asserted-by":"publisher","first-page":"e95","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(16):e95.","journal-title":"Nucleic Acids Res"},{"key":"967_CR4","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1093\/bioinformatics\/btq653","volume":"27","author":"L Ilie","year":"2011","unstructured":"Ilie L, Fazayeli F, Ilie S. HiTEC: accurate error correction in high- throughput sequencing data. Bioinformatics. 2011;27:295\u2013302.","journal-title":"Bioinformatics"},{"key":"967_CR5","doi-asserted-by":"publisher","first-page":"1284","DOI":"10.1093\/bioinformatics\/btq151","volume":"26","author":"L Salmela","year":"2010","unstructured":"Salmela L. Correction of sequencing errors in a mixed set of reads. Bioinformatics. 2010;26:1284\u201390.","journal-title":"Bioinformatics"},{"key":"967_CR6","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1093\/bib\/bbs015","volume":"14","author":"X Yang","year":"2013","unstructured":"Yang X, Chockalingam S, Aluru S. A survey of error correction methods for next generation sequencing. Brief Bioinform. 2013;14:56\u201366.","journal-title":"Brief Bioinform"},{"key":"967_CR7","doi-asserted-by":"publisher","first-page":"R116","DOI":"10.1186\/gb-2010-11-11-r116","volume":"11","author":"D Kelley","year":"2010","unstructured":"Kelley D, Schatz M, Salzberg L. Quake: quality-aware detection and correction of sequencing erros. Genome Biol. 2010;11:R116.","journal-title":"Genome Biol"},{"key":"967_CR8","doi-asserted-by":"publisher","first-page":"2157","DOI":"10.1093\/bioinformatics\/btp379","volume":"25","author":"J Schro der","year":"2009","unstructured":"Schro der J, Schro der H, Puglisi SJ, Sinha R, Schmidt B. SHREC: a short- read error correction method. Bioinformatics. 2009;25:2157\u201363.","journal-title":"Bioinformatics"},{"key":"967_CR9","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1186\/1471-2105-11-485","volume":"11","author":"MP Cox","year":"2010","unstructured":"Cox MP, Peterson DA, Biggs PJ. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics. 2010;11:485.","journal-title":"BMC Bioinformatics"},{"key":"967_CR10","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754\u201360.","journal-title":"Bioinformatics"},{"issue":"10","key":"967_CR11","doi-asserted-by":"publisher","first-page":"e26314","DOI":"10.1371\/journal.pone.0026314","volume":"6","author":"L Smeds","year":"2011","unstructured":"Smeds L, K\u00fcnstner A. ConDeTri - A Content Dependent Read Trimmer for Illumina Data. PLoS One. 2011;6(10):e26314.","journal-title":"PLoS One"},{"issue":"1","key":"967_CR12","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1186\/s12859-014-0366-2","volume":"15","author":"CC Lo","year":"2014","unstructured":"Lo CC, Chain PS. Rapid evaluation and quality control of next generation sequencing data with FaQCs. 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