{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T16:22:03Z","timestamp":1780330923122,"version":"3.54.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,11,16]],"date-time":"2018-11-16T00:00:00Z","timestamp":1542326400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["U1806205"],"award-info":[{"award-number":["U1806205"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Center for High Performance Computing and System Simulation, Pilot National Laboratory for Marine Science and Technology"},{"name":"Engineering Research Center of Digital Media Technology, Ministry of Education"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Modern bioinformatics tools for analyzing large-scale NGS datasets often need to include fast implementations of core sequence alignment algorithms in order to achieve reasonable execution times. We address this need by presenting the BGSA toolkit for optimized implementations of popular bit-parallel global pairwise alignment algorithms on modern microprocessors.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>BGSA outperforms Edlib, SeqAn and BitPAl for pairwise edit distance computations and Parasail, SeqAn and BitPAl when using more general scoring schemes for pairwise alignments of a batch of sequence reads on both standard multi-core CPUs and Xeon Phi many-core CPUs. Furthermore, banded edit distance performance of BGSA on a Xeon Phi-7210 outperforms the highly optimized NVBio implementation on a Titan X GPU for the seed verification stage of a read mapper by a factor of 4.4.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>BGSA is open-source and available at https:\/\/github.com\/sdu-hpcl\/BGSA.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty930","type":"journal-article","created":{"date-parts":[[2018,11,15]],"date-time":"2018-11-15T21:50:13Z","timestamp":1542318613000},"page":"2306-2308","source":"Crossref","is-referenced-by-count":24,"title":["BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures"],"prefix":"10.1093","volume":"35","author":[{"given":"Jikai","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Software, Shandong University, Jinan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haidong","family":"Lan","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University, Jinan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuandong","family":"Chan","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University, Jinan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Shang","sequence":"additional","affiliation":[{"name":"Supercomputer Center, Zhengzhou University, Zhengzhou City, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Informatik, Johannes Gutenberg University, Mainz, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiguo","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University, Jinan, China"},{"name":"National Supercomputing Center in Wuxi, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,11,16]]},"reference":[{"key":"2023051612113045200_bty930-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-016-0930-z","article-title":"Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments","volume":"17","author":"Daily","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2023051612113045200_bty930-B2","article-title":"Mason\u2013A Read simulator for second generation sequencing data","author":"Holtgrewe","year":"2010"},{"key":"2023051612113045200_bty930-B3","doi-asserted-by":"crossref","first-page":"3166","DOI":"10.1093\/bioinformatics\/btu507","article-title":"Bitpal: a bit-parallel, general integer-scoring sequence alignment algorithm","volume":"30","author":"Loving","year":"2014","journal-title":"Bioinformatics"},{"key":"2023051612113045200_bty930-B4","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1038\/nmeth.2221","article-title":"The gem mapper: fast, accurate and versatile alignment by filtration","volume":"9","author":"Marco-Sola","year":"2012","journal-title":"Nat. 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