Genpip: In-memory acceleration of genome analysis via tight integration of basecalling and read mapping

H Mao, M Alser, M Sadrosadati, C Firtina… - 2022 55th IEEE/ACM …, 2022 - ieeexplore.ieee.org
Nanopore sequencing is a widely-used high-throughput genome sequencing technology
that can sequence long fragments of a genome into raw electrical signals at low cost …

Helix: Algorithm/architecture co-design for accelerating nanopore genome base-calling

Q Lou, SC Janga, L Jiang - … of the ACM International Conference on …, 2020 - dl.acm.org
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 …

Accelerated nanopore basecalling with SLOW5 data format

H Samarakoon, JM Ferguson, H Gamaarachchi… - …, 2023 - academic.oup.com
Motivation Nanopore sequencing is emerging as a key pillar in the genomic technology
landscape but computational constraints limiting its scalability remain to be overcome. The …

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

H Teng, MD Cao, MB Hall, T Duarte, S Wang… - …, 2018 - academic.oup.com
Sequencing by translocating DNA fragments through an array of nanopores is a rapidly
maturing technology that offers faster and cheaper sequencing than other approaches …

A framework for designing efficient deep learning-based genomic basecallers

G Singh, M Alser, A Khodamoradi, K Denolf… - arXiv preprint arXiv …, 2022 - arxiv.org
Nanopore sequencing generates noisy electrical signals that need to be converted into a
standard string of DNA nucleotide bases using a computational step called basecalling. The …

RawAlign: Accurate, fast, and scalable raw nanopore signal mapping via combining seeding and alignment

J Lindegger, C Firtina, NM Ghiasi… - arXiv preprint arXiv …, 2023 - arxiv.org
Nanopore-based sequencers generate a series of raw electrical signal measurements that
represent the contents of a biological sequence molecule passing through the sequencer's …

Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling

M Pagès-Gallego, J de Ridder - Genome Biology, 2023 - Springer
Background Nanopore-based DNA sequencing relies on basecalling the electric current
signal. Basecalling requires neural networks to achieve competitive accuracies. To improve …

GenAx: A genome sequencing accelerator

D Fujiki, A Subramaniyan, T Zhang… - 2018 ACM/IEEE 45th …, 2018 - ieeexplore.ieee.org
Genomics can transform health-care through precision medicine. Plummeting sequencing
costs would soon make genome testing affordable to the masses. Compute efficiency …

RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes

C Firtina, N Mansouri Ghiasi, J Lindegger… - …, 2023 - academic.oup.com
Nanopore sequencers generate electrical raw signals in real-time while sequencing long
genomic strands. These raw signals can be analyzed as they are generated, providing an …

Gencache: Leveraging in-cache operators for efficient sequence alignment

A Nag, CN Ramachandra, R Balasubramonian… - Proceedings of the …, 2019 - dl.acm.org
Precision Medicine will rely on frequent genomic analysis, especially for patients
undergoing cancer treatments or suffering from rare diseases. Sequence alignment is …