{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T01:28:22Z","timestamp":1773278902323,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":527,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The storage and transmission of high-throughput sequencing data consumes significant resources. As our capacity to produce such data continues to increase, this burden will only grow. One approach to reduce storage and transmission requirements is to compress this sequencing data.<\/jats:p>\n               <jats:p>Results: We present a novel technique to boost the compression of sequencing that is based on the concept of bucketing similar reads so that they appear nearby in the file. We demonstrate that, by adopting a data-dependent bucketing scheme and employing a number of encoding ideas, we can achieve substantially better compression ratios than existing de novo sequence compression tools, including other bucketing and reordering schemes. Our method, Mince, achieves up to a 45% reduction in file sizes (28% on average) compared with existing state-of-the-art de novo compression schemes.<\/jats:p>\n               <jats:p>Availability and implementation: Mince is written in C++11, is open source and has been made available under the GPLv3 license. It is available at http:\/\/www.cs.cmu.edu\/\u223cckingsf\/software\/mince.<\/jats:p>\n               <jats:p>Contact: \u00a0carlk@cs.cmu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv248","type":"journal-article","created":{"date-parts":[[2015,4,25]],"date-time":"2015-04-25T01:51:42Z","timestamp":1429926702000},"page":"2770-2777","source":"Crossref","is-referenced-by-count":36,"title":["Data-dependent bucketing improves reference-free compression of sequencing reads"],"prefix":"10.1093","volume":"31","author":[{"given":"Rob","family":"Patro","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Stony Brook University, Stony Brook, NY 11794-4400, USA and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carl","family":"Kingsford","sequence":"additional","affiliation":[{"name":"2 Department Computational Biology, School of Computer Science, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,4,24]]},"reference":[{"key":"2023020202212245600_btv248-B1","doi-asserted-by":"crossref","DOI":"10.1109\/CSB.2002.1039352","article-title":"DNA sequence compression using the Burrows-Wheeler Transform","author":"Adjeroh","year":"2002"},{"key":"2023020202212245600_btv248-B2","doi-asserted-by":"crossref","DOI":"10.1109\/BIBM.2011.110","article-title":"No-reference compression of genomic data stored in fastq format","volume-title":"Bioinformatics and Biomedicine (BIBM), 2011","author":"Bhola","year":"2011"},{"key":"2023020202212245600_btv248-B3","doi-asserted-by":"crossref","first-page":"e59190","DOI":"10.1371\/journal.pone.0059190","article-title":"Compression of FASTQ and SAM format sequencing data","volume":"8","author":"Bonfield","year":"2013","journal-title":"PLoS One"},{"key":"2023020202212245600_btv248-B4","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1093\/bioinformatics\/btp319","article-title":"Data structures and compression algorithms for genomic sequence data","volume":"25","author":"Brandon","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020202212245600_btv248-B5","doi-asserted-by":"crossref","first-page":"e79871","DOI":"10.1371\/journal.pone.0079871","article-title":"Compression of structured high-throughput sequencing data","volume":"8","author":"Campagne","year":"2013","journal-title":"PLoS One"},{"key":"2023020202212245600_btv248-B6","doi-asserted-by":"crossref","first-page":"2130","DOI":"10.1093\/bioinformatics\/btu183","article-title":"Lossy compression of quality scores in genomic data","volume":"30","author":"C\u00e1novas","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020202212245600_btv248-B7","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1093\/bioinformatics\/btn582","article-title":"Human genomes as email attachments","volume":"25","author":"Christley","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020202212245600_btv248-B8","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1093\/bioinformatics\/bts173","article-title":"Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform","volume":"28","author":"Cox","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020202212245600_btv248-B9","doi-asserted-by":"crossref","first-page":"2979","DOI":"10.1093\/bioinformatics\/btr505","article-title":"Robust relative compression of genomes with random access","volume":"27","author":"Deorowicz","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020202212245600_btv248-B10","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1748-7188-8-25","article-title":"Data compression for sequencing data","volume":"8","author":"Deorowicz","year":"2013","journal-title":"Algorithms Mol. 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