{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,24]],"date-time":"2025-06-24T06:02:20Z","timestamp":1750744940387},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The growth of next-generation sequencing means that more effective and efficient archiving methods are needed to store the generated data for public dissemination and in anticipation of more mature analytical methods later. This article examines methods for compressing the quality score component of the data to partly address this problem.<\/jats:p>\n               <jats:p>Results: We compare several compression policies for quality scores, in terms of both compression effectiveness and overall efficiency. The policies employ lossy and lossless transformations with one of several coding schemes. Experiments show that both lossy and lossless transformations are useful, and that simple coding methods, which consume less computing resources, are highly competitive, especially when random access to reads is needed.<\/jats:p>\n               <jats:p>Availability and implementation: Our C++ implementation, released under the Lesser General Public License, is available for download at http:\/\/www.cb.k.u-tokyo.ac.jp\/asailab\/members\/rwan.<\/jats:p>\n               <jats:p>Contact: \u00a0rwan@cuhk.edu.hk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr689","type":"journal-article","created":{"date-parts":[[2011,12,15]],"date-time":"2011-12-15T02:00:11Z","timestamp":1323914411000},"page":"628-635","source":"Crossref","is-referenced-by-count":44,"title":["Transformations for the compression of FASTQ quality scores of next-generation sequencing data"],"prefix":"10.1093","volume":"28","author":[{"given":"Raymond","family":"Wan","sequence":"first","affiliation":[{"name":"1 Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Chiba-ken 277-8561, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan and 3Department of Computer Science and Software Engineering, University of Melbourne, Victoria 3010, Australia"},{"name":"1 Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Chiba-ken 277-8561, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan and 3Department of Computer Science and Software Engineering, University of Melbourne, Victoria 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vo Ngoc","family":"Anh","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Chiba-ken 277-8561, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan and 3Department of Computer Science and Software Engineering, University of Melbourne, Victoria 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kiyoshi","family":"Asai","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Chiba-ken 277-8561, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan and 3Department of Computer Science and Software Engineering, University of Melbourne, Victoria 3010, Australia"},{"name":"1 Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Chiba-ken 277-8561, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan and 3Department of Computer Science and Software Engineering, University of Melbourne, Victoria 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,12,13]]},"reference":[{"key":"2023012512193497400_B1","doi-asserted-by":"crossref","first-page":"1783","DOI":"10.1093\/bioinformatics\/btq281","article-title":"Manipulation of FASTQ data with Galaxy","volume":"26","author":"Blankenberg","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512193497400_B2","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","article-title":"The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants","volume":"38","author":"Cock","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512193497400_B3","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1186\/1471-2105-11-514","article-title":"Data structures and compression algorithms for high-throughput sequencing technologies","volume":"11","author":"Daily","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012512193497400_B4","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1093\/bioinformatics\/btr014","article-title":"Compression of genomic sequences in FASTQ format","volume":"27","author":"Deorowicz","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512193497400_B5","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","article-title":"Base-calling of automated sequencer traces using Phred. 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