{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T03:53:25Z","timestamp":1772078005572,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2022,5,17]],"date-time":"2022-05-17T00:00:00Z","timestamp":1652745600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Key Research and Development Project","award":["2019YFE0109600"],"award-info":[{"award-number":["2019YFE0109600"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61871272"],"award-info":[{"award-number":["61871272"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017607","name":"Shenzhen Fundamental Research Program","doi-asserted-by":"publisher","award":["JCYJ20190808173617147"],"award-info":[{"award-number":["JCYJ20190808173617147"]}],"id":[{"id":"10.13039\/501100017607","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BGIShenzhen","award":["BGIRSZ20200002"],"award-info":[{"award-number":["BGIRSZ20200002"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,13]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>The data deluge of high-throughput sequencing (HTS) has posed great challenges to data storage and transfer. Many specific compression tools have been developed to solve this problem. However, most of the existing compressors are based on central processing unit (CPU) platform, which might be inefficient and expensive to handle large-scale HTS data. With the popularization of graphics processing units (GPUs), GPU-compatible sequencing data compressors become desirable to exploit the computing power of GPUs.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present a GPU-accelerated reference-free read compressor, namely CURC, for FASTQ files. Under a GPU\u2013CPU heterogeneous parallel scheme, CURC implements highly efficient lossless compression of DNA stream based on the pseudogenome approach and CUDA library. CURC achieves 2\u20136-fold speedup of the compression with competitive compression rate, compared with other state-of-the-art reference-free read compressors.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>CURC can be downloaded from https:\/\/github.com\/BioinfoSZU\/CURC.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac333","type":"journal-article","created":{"date-parts":[[2022,5,17]],"date-time":"2022-05-17T12:06:11Z","timestamp":1652789171000},"page":"3294-3296","source":"Crossref","is-referenced-by-count":7,"title":["CURC: a CUDA-based reference-free read compressor"],"prefix":"10.1093","volume":"38","author":[{"given":"Shaohui","family":"Xie","sequence":"first","affiliation":[{"name":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaotian","family":"He","sequence":"additional","affiliation":[{"name":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shan","family":"He","sequence":"additional","affiliation":[{"name":"School of Computer Science, University of Birmingham , Birmingham B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8479-6904","authenticated-orcid":false,"given":"Zexuan","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China"},{"name":"BGI-Shenzhen , Shenzhen 518083, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,17]]},"reference":[{"key":"2023041408201902500_","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1093\/bioinformatics\/btx639","article-title":"Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis","volume":"34","author":"Chandak","year":"2018","journal-title":"Bioinformatics"},{"key":"2023041408201902500_","doi-asserted-by":"crossref","first-page":"2674","DOI":"10.1093\/bioinformatics\/bty1015","article-title":"SPRING: a next-generation compressor for FASTQ data","volume":"35","author":"Chandak","year":"2019","journal-title":"Bioinformatics"},{"key":"2023041408201902500_","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1093\/bioinformatics\/bty670","article-title":"copMEM: finding maximal exact matches via sampling both genomes","volume":"35","author":"Grabowski","year":"2019","journal-title":"Bioinformatics"},{"key":"2023041408201902500_","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1093\/bioinformatics\/btz919","article-title":"PgRC: pseudogenome-based read compressor","volume":"36","author":"Kowalski","year":"2020","journal-title":"Bioinformatics"},{"key":"2023041408201902500_","author":"Kowalski","year":"2020"},{"key":"2023041408201902500_","doi-asserted-by":"crossref","first-page":"e1009229","DOI":"10.1371\/journal.pcbi.1009229","article-title":"Hamming-Shifting graph of genomic short reads: efficient construction and its application for compression","volume":"17","author":"Liu","year":"2021","journal-title":"PLoS Comput. 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