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Article: MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)

TitleMICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)
Authors
Issue Date2015
Citation
BMC Bioinformatics, 2015, v. 16 n. suppl. 7, article no. S10 How to Cite?
AbstractBackground: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alterative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC boards to offer ~55 PFLOPS. The CPU-like architecture of MIC allows CPU-based software to be parallelized easily; however, the performance is often inferior to GPU counterparts as an MIC card contains only ~60 cores (while a GPU card typically has over a thousand cores). Results: To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core. By utilizing the 512-bit vector units in the MIC and implementing a new seeding strategy, experiments on aligning 150 bp paired-end reads show that MICA using one MIC card is 4.9 times faster than BWA-MEM (using 6 cores of a top-end CPU), and slightly faster than SOAP3-dp (using a GPU). Furthermore, MICA's simplicity allows very efficient scale-up when multiple MIC cards are used in a node (3 cards give a 14.1-fold speedup over BWA-MEM). Summary: MICA can be readily used by MIC-enabled supercomputers for production purpose. We have tested MICA on Tianhe-2 with 90 WGS samples (17.47 Tera-bases), which can be aligned in an hour using 400 nodes. MICA has impressive performance even though MIC is only in its initial stage of development. Availability and implementation: MICA's source code is freely available at http://sourceforge.net/projects/mica-aligner under GPL v3. Supplementary information: Supplementary information is available as "Additional File 1". Datasets are available at www.bio8.cs.hku.hk/dataset/mica.
Persistent Identifierhttp://hdl.handle.net/10722/215514
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLUO, R-
dc.contributor.authorCHAN, SH-
dc.contributor.authorLAW, WC-
dc.contributor.authorHe, G-
dc.contributor.authorYu, C-
dc.contributor.authorLIU, CM-
dc.contributor.authorZhou, D-
dc.contributor.authorLi, Y-
dc.contributor.authorLi, R-
dc.contributor.authorWang, J-
dc.contributor.authorZhu, X-
dc.contributor.authorPeng, S-
dc.contributor.authorLam, TW-
dc.date.accessioned2015-08-21T13:28:36Z-
dc.date.available2015-08-21T13:28:36Z-
dc.date.issued2015-
dc.identifier.citationBMC Bioinformatics, 2015, v. 16 n. suppl. 7, article no. S10-
dc.identifier.urihttp://hdl.handle.net/10722/215514-
dc.description.abstractBackground: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alterative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC boards to offer ~55 PFLOPS. The CPU-like architecture of MIC allows CPU-based software to be parallelized easily; however, the performance is often inferior to GPU counterparts as an MIC card contains only ~60 cores (while a GPU card typically has over a thousand cores). Results: To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core. By utilizing the 512-bit vector units in the MIC and implementing a new seeding strategy, experiments on aligning 150 bp paired-end reads show that MICA using one MIC card is 4.9 times faster than BWA-MEM (using 6 cores of a top-end CPU), and slightly faster than SOAP3-dp (using a GPU). Furthermore, MICA's simplicity allows very efficient scale-up when multiple MIC cards are used in a node (3 cards give a 14.1-fold speedup over BWA-MEM). Summary: MICA can be readily used by MIC-enabled supercomputers for production purpose. We have tested MICA on Tianhe-2 with 90 WGS samples (17.47 Tera-bases), which can be aligned in an hour using 400 nodes. MICA has impressive performance even though MIC is only in its initial stage of development. Availability and implementation: MICA's source code is freely available at http://sourceforge.net/projects/mica-aligner under GPL v3. Supplementary information: Supplementary information is available as "Additional File 1". Datasets are available at www.bio8.cs.hku.hk/dataset/mica.-
dc.languageeng-
dc.relation.ispartofBMC Bioinformatics-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleMICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)-
dc.typeArticle-
dc.identifier.emailHe, G: gzhe2@HKUCC-COM.hku.hk-
dc.identifier.emailLam, TW: twlam@cs.hku.hk-
dc.identifier.authorityLam, TW=rp00135-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1471-2105-16-S7-S10-
dc.identifier.pmid25952019-
dc.identifier.scopuseid_2-s2.0-84977534075-
dc.identifier.hkuros248453-
dc.identifier.volume16-
dc.identifier.issuesuppl. 7-
dc.identifier.spagearticle no. S10-
dc.identifier.epagearticle no. S10-
dc.identifier.isiWOS:000353976600010-

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