Nanopore Base Calling on the Edge
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. Availability: https://github.com/fmfi-compbio/coral-basecaller
Code (1)
Tasks
speech-recognitionSpeech RecognitionMethods 이 논문이 사용한 방법론
Similar Papers 제목 키워드 기반
Helix: Algorithm/Architecture Co-design for Accelerating Nanopore Genome Base-calling
Nanopore genome sequencing is the key to enabling personalized medicine, global food security, and virus surveillance. The state-of-the-art base-callers adopt deep neural networks (DNNs) to translate electrical signals g…
Dynamic Pooling Improves Nanopore Base Calling Accuracy
In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-trivial task, and its quality has a large …
GPUModelling the nanopore sequencing process with Helicase HMMs
Recent advancements in nanopore sequencing technology, particularly the R10 nanopore from Oxford Nanopore Technology, have necessitated the development of improved data processing methods to utilize their potential for m…
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art basecallers employ complex deep learnin…
CRANE: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models
Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly.…