{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T23:55:04Z","timestamp":1772236504304,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008383","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,11,19]],"date-time":"2020-11-19T00:00:00Z","timestamp":1605744000000}}],"reference-count":33,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2020,11,9]],"date-time":"2020-11-09T00:00:00Z","timestamp":1604880000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>In large DNA sequence repositories, archival data storage is often coupled with computers that provide 40 or more CPU threads and multiple GPU (general-purpose graphics processing unit) devices. This presents an opportunity for DNA sequence alignment software to exploit high-concurrency hardware to generate short-read alignments at high speed. Arioc, a GPU-accelerated short-read aligner, can compute WGS (whole-genome sequencing) alignments ten times faster than comparable CPU-only alignment software. When two or more GPUs are available, Arioc's speed increases proportionately because the software executes concurrently on each available GPU device. We have adapted Arioc to recent multi-GPU hardware architectures that support high-bandwidth peer-to-peer memory accesses among multiple GPUs. By modifying Arioc's implementation to exploit this GPU memory architecture we obtained a further 1.8x-2.9x increase in overall alignment speeds. With this additional acceleration, Arioc computes two million short-read alignments per second in a four-GPU system; it can align the reads from a human WGS sequencer run\u2013over 500 million 150nt paired-end reads\u2013in less than 15 minutes. As WGS data accumulates exponentially and high-concurrency computational resources become widespread, Arioc addresses a growing need for timely computation in the short-read data analysis toolchain.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008383","type":"journal-article","created":{"date-parts":[[2020,11,9]],"date-time":"2020-11-09T18:49:23Z","timestamp":1604947763000},"page":"e1008383","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Arioc: High-concurrency short-read alignment on multiple GPUs"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1263-5532","authenticated-orcid":true,"given":"Richard","family":"Wilton","sequence":"first","affiliation":[]},{"given":"Alexander S.","family":"Szalay","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,11,9]]},"reference":[{"issue":"7","key":"pcbi.1008383.ref001","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pbio.1002195","article-title":"Big Data: Astronomical or Genomical?","volume":"13","author":"ZD Stephens","year":"2015","journal-title":"PLoS Biol"},{"issue":"4","key":"pcbi.1008383.ref002","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1038\/nrg.2017.113","article-title":"Cloud Computing for Genomic Data Analysis and Collaboration","volume":"19","author":"B Langmead","year":"2018","journal-title":"Nat Rev Genet"},{"key":"pcbi.1008383.ref003","doi-asserted-by":"crossref","first-page":"e808","DOI":"10.7717\/peerj.808","article-title":"Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space","volume":"3","author":"R Wilton","year":"2015","journal-title":"PeerJ"},{"key":"pcbi.1008383.ref004","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bioinformatics\/bty167","article-title":"Arioc: GPU-accelerated alignment of short bisulfite-treated reads","volume":"34","author":"R Wilton","year":"2018","journal-title":"Bioinformatics"},{"issue":"5","key":"pcbi.1008383.ref005","doi-asserted-by":"crossref","first-page":"e65632","DOI":"10.1371\/journal.pone.0065632","article-title":"SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner","volume":"8","author":"R Luo","year":"2013","journal-title":"PLoS One"},{"key":"pcbi.1008383.ref006","unstructured":"Li H. 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