Computational Biology
@ Comenius University in Bratislava

Peter Perešíni, Vladimír Boža, Broňa Brejová, Tomáš Vinař. Nanopore Base Calling on the Edge. Technical Report 2011.04312, arXiv, 2020.

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Download from publisher: https://arxiv.org/pdf/2011.04312

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Abstract:

We developed a new base caller DeepNano-coral for nanopore sequencing, which 
is optimized to run on the Coral Edge Tensor Processing Unit, a small USB-
attached hardware accelerator. To achieve this goal, we have designed new 
versions of two key components used in convolutional neural networks for 
speech recognition and base calling. In our components, we propose a new way 
of factorization of a full convolution into smaller operations, which 
decreases memory access operations, memory access being a bottleneck on this 
device. DeepNano-coral achieves real-time base calling during sequencing 
with the accuracy slightly better than the fast mode of the Guppy base 
caller and is extremely energy efficient, using only 10W of power.