{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T03:53:14Z","timestamp":1772077994676,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the sequences themselves. By aggregating a set of reads into a compressed index, we find that the majority of bases can be predicted from the sequence of bases that are adjacent to them and, hence, are likely to be less informative for variant calling or other applications. The quality scores for such bases are aggressively compressed, leaving a relatively small number at full resolution. As our approach relies directly on redundancy present in the reads, it does not need a reference sequence and is, therefore, applicable to data from metagenomics and de novo experiments as well as to re-sequencing data.<\/jats:p>\n               <jats:p>Results: We show that a conservative smoothing strategy affecting 75% of the quality scores above Q2 leads to an overall quality score compression of 1 bit per value with a negligible effect on variant calling. A compression of 0.68 bit per quality value is achieved using a more aggressive smoothing strategy, again with a very small effect on variant calling.<\/jats:p>\n               <jats:p>Availability: Code to construct the BWT and LCP-array on large genomic data sets is part of the BEETL library, available as a github repository at git@github.com:BEETL\/BEETL.git.<\/jats:p>\n               <jats:p>Contact: \u00a0acox@illumina.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt257","type":"journal-article","created":{"date-parts":[[2013,5,10]],"date-time":"2013-05-10T04:33:54Z","timestamp":1368160434000},"page":"24-30","source":"Crossref","is-referenced-by-count":28,"title":["Adaptive reference-free compression of sequence quality scores"],"prefix":"10.1093","volume":"30","author":[{"given":"Lilian","family":"Janin","sequence":"first","affiliation":[{"name":"1 Computational Biology Group, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK and 2Dipartimento di Matematica e Informatica, University of Palermo, Via Archirafi 34, 90123 Palermo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giovanna","family":"Rosone","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK and 2Dipartimento di Matematica e Informatica, University of Palermo, Via Archirafi 34, 90123 Palermo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony J.","family":"Cox","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK and 2Dipartimento di Matematica e Informatica, University of Palermo, Via Archirafi 34, 90123 Palermo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,5,9]]},"reference":[{"key":"2023012710375024800_btt257-B1","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-78909-5","volume-title":"The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching","author":"Adjeroh","year":"2008","edition":"1st edn"},{"key":"2023012710375024800_btt257-B2","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-14-S5-S2","article-title":"metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences","volume":"14","author":"Ander","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023012710375024800_btt257-B3","first-page":"219","article-title":"Lightweight BWT construction for very large string collections","volume-title":"CPM 2011, volume 6661 of LNCS","author":"Bauer","year":"2011"},{"key":"2023012710375024800_btt257-B4","first-page":"326","article-title":"Lightweight LCP construction for next-generation sequencing datasets","volume-title":"WABI 2012, volume 7534 LNBI of LNCS","author":"Bauer","year":"2012"},{"key":"2023012710375024800_btt257-B5","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.tcs.2012.02.002","article-title":"Lightweight algorithms for constructing and inverting the BWT of string collections","volume":"483","author":"Bauer","year":"2013","journal-title":"Theor. 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