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GPU-Accelerated Genome Assembly: A Deep Dive into Clara Genomics Analysis SDK

Andreas Hehn, NVIDIA | Milos Maric, NVIDIA | Mike Vella, NVIDIA

GTC 2020

We'll present de novo genome assembly for long DNA reads using the Clara Genomics Analysis SDK and dig deep into the SDK implementation. We'll discuss the suitability of GPUs for genomics workloads and present algorithms suitable for massively parallel systems. We'll also review the challenges we faced while implementing the algorithms in CUDA, and present the solutions used in cudaAligner, cudaPoa, and cudamapper.