{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T07:02:35Z","timestamp":1761807755350},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes &amp;lt; 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers.<\/jats:p>\n               <jats:p>Availability: SOAP3 is available at: http:\/\/www.cs.hku.hk\/2bwt-tools\/soap3; http:\/\/soap.genomics.org.cn\/soap3.html.<\/jats:p>\n               <jats:p>Contact: \u00a0liruiqiang@gmail.com, twlam@cs.hku.hk<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts061","type":"journal-article","created":{"date-parts":[[2012,1,29]],"date-time":"2012-01-29T01:14:57Z","timestamp":1327799697000},"page":"878-879","source":"Crossref","is-referenced-by-count":180,"title":["SOAP3: ultra-fast GPU-based parallel alignment tool for short reads"],"prefix":"10.1093","volume":"28","author":[{"given":"Chi-Man","family":"Liu","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Thomas","family":"Wong","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Edward","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Ruibang","family":"Luo","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Siu-Ming","family":"Yiu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Yingrui","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Bingqiang","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Chang","family":"Yu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Xiaowen","family":"Chu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Kaiyong","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Ruiqiang","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]},{"given":"Tak-Wah","family":"Lam","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Hong Kong, 2BGI Shenzhen, China, 3Department of Computer Science, Hong Kong Baptist University, Hong Kong and 4Peking-Tsinghua Center for Life Sciences, Biodynamics Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China"}]}],"member":"286","published-online":{"date-parts":[[2012,1,28]]},"reference":[{"key":"2023012512200278200_B1","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1093\/bioinformatics\/btr151","article-title":"Exact and complete short read alignment to microbial genomes using gpu 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