DeepNano: deep recurrent neural networks for base calling in MinION nanopore reads
The MinION device by Oxford Nanopore produces very long reads (reads over 100 kBp
were reported); however it suffers from high sequencing error rate. We present an open …
were reported); however it suffers from high sequencing error rate. We present an open …
Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias
R Krishnakumar, A Sinha, SW Bird, H Jayamohan… - Scientific reports, 2018 - nature.com
Emerging sequencing technologies are allowing us to characterize environmental, clinical
and laboratory samples with increasing speed and detail, including real-time analysis and …
and laboratory samples with increasing speed and detail, including real-time analysis and …
Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning
Sequencing by translocating DNA fragments through an array of nanopores is a rapidly
maturing technology that offers faster and cheaper sequencing than other approaches …
maturing technology that offers faster and cheaper sequencing than other approaches …
Nanopore base calling on the edge
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 …
the field with features including monitoring of run progress and selective sequencing. To …
Accelerated nanopore basecalling with SLOW5 data format
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 …
landscape but computational constraints limiting its scalability remain to be overcome. The …
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 …
signal. Basecalling requires neural networks to achieve competitive accuracies. To improve …
Nanocall: an open source basecaller for Oxford Nanopore sequencing data
Abstract Motivation The highly portable Oxford Nanopore MinION sequencer has enabled
new applications of genome sequencing directly in the field. However, the MinION currently …
new applications of genome sequencing directly in the field. However, the MinION currently …
Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing
J Silvestre-Ryan, I Holmes - Genome biology, 2021 - Springer
We develop a general computational approach for improving the accuracy of basecalling
with Oxford Nanopore's 1D 2 and related sequencing protocols. Our software PoreOver …
with Oxford Nanopore's 1D 2 and related sequencing protocols. Our software PoreOver …
Performance of neural network basecalling tools for Oxford Nanopore sequencing
Background Basecalling, the computational process of translating raw electrical signal to
nucleotide sequence, is of critical importance to the sequencing platforms produced by …
nucleotide sequence, is of critical importance to the sequencing platforms produced by …
Causalcall: Nanopore basecalling using a temporal convolutional network
Nanopore sequencing is promising because of its long read length and high speed. During
sequencing, a strand of DNA/RNA passes through a biological nanopore, which causes the …
sequencing, a strand of DNA/RNA passes through a biological nanopore, which causes the …