Computational Biology
@ Comenius University in Bratislava

Peter Peresini, Vladimir Boza, Brona Brejova, Tomas Vinar. Nanopore Base Calling on the Edge. Bioinformatics, 37(24):4661-4667. 2021.

Download preprint: not available

Download from publisher: https://dx.doi.org/10.1093/bioinformatics/btab528

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Bibliography entry: BibTeX

See also: early version

Abstract:

MOTIVATION: MinION is a portable nanopore sequencing device that can be easily
operated in the field with features including monitoring of run progress and
selective sequencing. To fully exploit these features, real-time base calling is 
required. Up to date, this has only been achieved at the cost of high computing
requirements that pose limitations in terms of hardware availability in common
laptops and energy consumption. RESULTS: 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 10 W of power.
AVAILABILITY: https://github.com/fmfi-compbio/coral-basecaller. SUPPLEMENTARY
INFORMATION: Supplementary data are available at Bioinformatics online.