11605
Usman Roshan
Exact short read mapping to whole genomes with the Smith-Waterman algorithm is computationally expensive yet highly accurate when aligning reads with mismatches and gaps. We introduce a GPU program called MaxSSmap with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. Similar to mainstream approaches MaxSSmap identifies a local region of the […]
View View   Download Download (PDF)   
Abdullah Gharaibeh, Matei Ripeanu
GPUs offer drastically different performance characteristics compared to traditional multicore architectures. To explore the tradeoffs exposed by this difference, we refactor MUMmer, a widely-used, highly-engineered bioinformatics application which has both CPU- and GPU-based implementations. We synthesize our experience as three high-level guidelines to design efficient GPU-based applications. First, minimizing the communication overheads is as important […]
Cole Trapnell, Michael C. Schatz
MUMmerGPU uses highly-parallel commodity graphics processing units (GPU) to accelerate the data-intensive computation of aligning next generation DNA sequence data to a reference sequence for use in diverse applications such as disease genotyping and personal genomics. MUMmerGPU 2.0 features a new stackless depth-first-search print kernel and is 13× faster than the serial CPU version of […]

* * *

* * *

Follow us on Twitter

HGPU group

1746 peoples are following HGPU @twitter

Like us on Facebook

HGPU group

371 people like HGPU on Facebook

HGPU group © 2010-2016 hgpu.org

All rights belong to the respective authors

Contact us: