{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T20:40:40Z","timestamp":1765485640566},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1490,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The explosive growth of next-generation sequencing datasets poses a challenge to the mapping of reads to reference genomes in terms of alignment quality and execution speed. With the continuing progress of high-throughput sequencing technologies, read length is constantly increasing and many existing aligners are becoming inefficient as generated reads grow larger.<\/jats:p>\n               <jats:p>Results: We present CUSHAW2, a parallelized, accurate, and memory-efficient long read aligner. Our aligner is based on the seed-and-extend approach and uses maximal exact matches as seeds to find gapped alignments. We have evaluated and compared CUSHAW2 to the three other long read aligners BWA-SW, Bowtie2 and GASSST, by aligning simulated and real datasets to the human genome. The performance evaluation shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads.<\/jats:p>\n               <jats:p>Availability: CUSHAW2, written in C++, and all simulated datasets are available at http:\/\/cushaw2.sourceforge.net<\/jats:p>\n               <jats:p>Contact: \u00a0liuy@uni-mainz.de; bertil.schmidt@uni-mainz.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts414","type":"journal-article","created":{"date-parts":[[2012,9,7]],"date-time":"2012-09-07T20:35:22Z","timestamp":1347050122000},"page":"i318-i324","source":"Crossref","is-referenced-by-count":80,"title":["Long read alignment based on maximal exact match seeds"],"prefix":"10.1093","volume":"28","author":[{"given":"Yongchao","family":"Liu","sequence":"first","affiliation":[{"name":"Institut f\u00fcr Informatik, Johannes Gutenberg Universit\u00e4t Mainz, Mainz 55099, Germany."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Informatik, Johannes Gutenberg Universit\u00e4t Mainz, Mainz 55099, Germany."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,9,3]]},"reference":[{"key":"2023012513035460900_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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