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BMC Bioinformatics. 2015;16 Suppl 7:S10. doi: 10.1186/1471-2105-16-S7-S10. Epub 2015 Apr 23.

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

Abstract

BACKGROUND:

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.

PMID:
25952019
PMCID:
PMC4423751
DOI:
10.1186/1471-2105-16-S7-S10
[Indexed for MEDLINE]
Free PMC Article

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