Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data.

ABSTRACT:

Background

Despite recent progress in basecalling of Oxford nanopore DNA sequencing data, its wide adoption is still being hampered by its relatively low accuracy compared to short read technologies. Furthermore, very little of the recent research was focused on basecalling of RNA data, which has different characteristics than its DNA counterpart.

Results

We fill this gap by benchmarking a fully convolutional deep learning basecalling architecture with improved performance compared to Oxford nanopore's RNA basecallers.

Availability

The source code for our basecaller is available at: https://github.com/biodlab/RODAN .

SUBMITTER: Neumann D

PROVIDER: S-EPMC9020074 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data.

Neumann Don D Reddy Anireddy S N ASN Ben-Hur Asa A

BMC bioinformatics 20220420 1

<h4>Background</h4>Despite recent progress in basecalling of Oxford nanopore DNA sequencing data, its wide adoption is still being hampered by its relatively low accuracy compared to short read technologies. Furthermore, very little of the recent research was focused on basecalling of RNA data, which has different characteristics than its DNA counterpart.<h4>Results</h4>We fill this gap by benchmarking a fully convolutional deep learning basecalling architecture with improved performance compare ...[more]

PMID: 35443610

Similar Datasets

Training Data Diversity Enhances the Basecalling of Novel RNA Modification-Induced Nanopore Sequencing Readouts.

Project description:Accurately basecalling sequence backbones in the presence of nucleotide modifications remains a substantial challenge in nanopore sequencing bioinformatics. It has been extensively demonstrated that state-of-the-art basecallers are less compatible with modification-induced sequencing signals. A precise basecalling, on the other hand, serves as the prerequisite for virtually all the downstream analyses. Here, we report that basecallers exposed to diverse training modifications gain the generalizability to analyze novel modifications. With synthesized oligos as the model system, we precisely basecall various out-of-sample RNA modifications. From the representation learning perspective, we attribute this generalizability to basecaller representation space expanded by diverse training modifications. Taken together, we conclude increasing the training data diversity as a novel paradigm for building modification-tolerant nanopore sequencing basecallers.

| S-EPMC11383704 | biostudies-literature

Causalcall: Nanopore Basecalling Using a Temporal Convolutional Network.

Project description: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 current in the pore to fluctuate. During basecalling, context-dependent current measurements are translated into the base sequence of the DNA/RNA strand. Accurate and fast basecalling is vital for downstream analyses such as genome assembly and detecting single-nucleotide polymorphisms and genomic structural variants. However, owing to the various changes in DNA/RNA molecules, noise during sequencing, and limitations of basecalling methods, accurate basecalling remains a challenge. In this paper, we propose Causalcall, which uses an end-to-end temporal convolution-based deep learning model for accurate and fast nanopore basecalling. Developed on a temporal convolutional network (TCN) and a connectionist temporal classification decoder, Causalcall directly identifies base sequences of varying lengths from current measurements in long time series. In contrast to the basecalling models using recurrent neural networks (RNNs), the convolution-based model of Causalcall can speed up basecalling by matrix computation. Experiments on multiple species have demonstrated the great potential of the TCN-based model to improve basecalling accuracy and speed when compared to an RNN-based model. Besides, experiments on genome assembly indicate the utility of Causalcall in reference-based genome assembly.

| S-EPMC6984161 | biostudies-literature

Accelerated nanopore basecalling with SLOW5 data format.

Project description:MotivationNanopore sequencing is emerging as a key pillar in the genomic technology landscape but computational constraints limiting its scalability remain to be overcome. The translation of raw current signal data into DNA or RNA sequence reads, known as 'basecalling', is a major friction in any nanopore sequencing workflow. Here, we exploit the advantages of the recently developed signal data format 'SLOW5' to streamline and accelerate nanopore basecalling on high-performance computing (HPC) and cloud environments.ResultsSLOW5 permits highly efficient sequential data access, eliminating a potential analysis bottleneck. To take advantage of this, we introduce Buttery-eel, an open-source wrapper for Oxford Nanopore's Guppy basecaller that enables SLOW5 data access, resulting in performance improvements that are essential for scalable, affordable basecalling.Availability and implementationButtery-eel is available at https://github.com/Psy-Fer/buttery-eel.

| S-EPMC10261880 | biostudies-literature

The Precise Basecalling of Short-Read Nanopore Sequencing.

Project description:The nanopore sequencing of short sequences, whose lengths are typically less than 0.3kb therefore comparable with Illumina sequencing techniques, has recently gained wide attention. Here, we design a scheme for training nanopore basecallers that are specialized for short biomolecules. With bioengineered RNA (BioRNA) molecules as examples, we demonstrate the superior accuracy of basecallers trained by our scheme.

| S-EPMC11429927 | biostudies-literature

Performance of neural network basecalling tools for Oxford Nanopore sequencing.

Project description:BackgroundBasecalling, the computational process of translating raw electrical signal to nucleotide sequence, is of critical importance to the sequencing platforms produced by Oxford Nanopore Technologies (ONT). Here, we examine the performance of different basecalling tools, looking at accuracy at the level of bases within individual reads and at majority-rule consensus basecalls in an assembly. We also investigate some additional aspects of basecalling: training using a taxon-specific dataset, using a larger neural network model and improving consensus basecalls in an assembly by additional signal-level analysis with Nanopolish.ResultsTraining basecallers on taxon-specific data results in a significant boost in consensus accuracy, mostly due to the reduction of errors in methylation motifs. A larger neural network is able to improve both read and consensus accuracy, but at a cost to speed. Improving consensus sequences ('polishing') with Nanopolish somewhat negates the accuracy differences in basecallers, but pre-polish accuracy does have an effect on post-polish accuracy.ConclusionsBasecalling accuracy has seen significant improvements over the last 2 years. The current version of ONT's Guppy basecaller performs well overall, with good accuracy and fast performance. If higher accuracy is required, users should consider producing a custom model using a larger neural network and/or training data from the same species.

| S-EPMC6591954 | biostudies-literature

Estimated Nucleotide Reconstruction Quality Symbols of Basecalling Tools for Oxford Nanopore Sequencing.

Project description:Currently, one of the fastest-growing DNA sequencing technologies is nanopore sequencing. One of the key stages involved in processing sequencer data is the basecalling process, where the input sequence of currents measured on the nanopores of the sequencer reproduces the DNA sequences, called DNA reads. Many of the applications dedicated to basecalling, together with the DNA sequence, provide the estimated quality of the reconstruction of a given nucleotide (quality symbols are contained on every fourth line of the FASTQ file; each nucleotide in the FASTQ file corresponds to exactly one estimated nucleotide reconstruction quality symbol). Herein, we compare the estimated nucleotide reconstruction quality symbols (signs from every fourth line of the FASTQ file) reported by other basecallers. The conducted experiments consisted of basecalling the same raw datasets from the nanopore device by other basecallers and comparing the provided quality symbols, denoting the estimated quality of the nucleotide reconstruction. The results show that the estimated quality reported by different basecallers may vary, depending on the tool used, particularly in terms of range and distribution. Moreover, we mapped basecalled DNA reads to reference genomes and calculated matched and mismatched rates for groups of nucleotides with the same quality symbol. Finally, the presented paper shows that the estimated nucleotide reconstruction quality reported in the basecalling process is not used in any investigated tool for processing nanopore DNA reads.

| S-EPMC10422362 | biostudies-literature

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

Project description:BackgroundNanopore-based DNA sequencing relies on basecalling the electric current signal. Basecalling requires neural networks to achieve competitive accuracies. To improve sequencing accuracy further, new models are continuously proposed with new architectures. However, benchmarking is currently not standardized, and evaluation metrics and datasets used are defined on a per publication basis, impeding progress in the field. This makes it impossible to distinguish data from model driven improvements.ResultsTo standardize the process of benchmarking, we unified existing benchmarking datasets and defined a rigorous set of evaluation metrics. We benchmarked the latest seven basecaller models by recreating and analyzing their neural network architectures. Our results show that overall Bonito's architecture is the best for basecalling. We find, however, that species bias in training can have a large impact on performance. Our comprehensive evaluation of 90 novel architectures demonstrates that different models excel at reducing different types of errors and using recurrent neural networks (long short-term memory) and a conditional random field decoder are the main drivers of high performing models.ConclusionsWe believe that our work can facilitate the benchmarking of new basecaller tools and that the community can further expand on this work.

| S-EPMC10088207 | biostudies-literature

Adapting Nanopore Sequencing Basecalling Models for Modification Detection via Incremental Learning and Anomaly Detection.

Project description:We leverage machine learning approaches to adapt nanopore sequencing basecallers for nucleotide modification detection. We first apply the incremental learning technique to improve the basecalling of modification-rich sequences, which are usually of high biological interests. With sequence backbones resolved, we further run anomaly detection on individual nucleotides to determine their modification status. By this means, our pipeline promises the single-molecule, single-nucleotide and sequence context-free detection of modifications. We benchmark the pipeline using control oligos, further apply it in the basecalling of densely-modified yeast tRNAs and E.coli genomic DNAs, the cross-species detection of N6-methyladenosine (m6A) in mammalian mRNAs, and the simultaneous detection of N1-methyladenosine (m1A) and m6A in human mRNAs. Our IL-AD workflow is available at: https://github.com/wangziyuan66/IL-AD.

| S-EPMC10769248 | biostudies-literature

Adapting nanopore sequencing basecalling models for modification detection via incremental learning and anomaly detection.

Project description:We leverage machine learning approaches to adapt nanopore sequencing basecallers for nucleotide modification detection. We first apply the incremental learning (IL) technique to improve the basecalling of modification-rich sequences, which are usually of high biological interest. With sequence backbones resolved, we further run anomaly detection (AD) on individual nucleotides to determine their modification status. By this means, our pipeline promises the single-molecule, single-nucleotide, and sequence context-free detection of modifications. We benchmark the pipeline using control oligos, further apply it in the basecalling of densely-modified yeast tRNAs and E.coli genomic DNAs, the cross-species detection of N6-methyladenosine (m6A) in mammalian mRNAs, and the simultaneous detection of N1-methyladenosine (m1A) and m6A in human mRNAs. Our IL-AD workflow is available at: https://github.com/wangziyuan66/IL-AD .

| S-EPMC11339354 | biostudies-literature

Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data.

Project description:Compared with second-generation sequencing technologies, third-generation single-molecule RNA sequencing has unprecedented advantages; the long reads it generates facilitate isoform-level transcript characterization. In particular, the Oxford Nanopore Technology sequencing platforms have become more popular in recent years owing to their relatively high affordability and portability compared with other third-generation sequencing technologies. To aid the development of analytical tools that leverage the power of this technology, simulated data provide a cost-effective solution with ground truth. However, a nanopore sequence simulator targeting transcriptomic data is not available yet. We introduce Trans-NanoSim, a tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-sequncing data. We comprehensively benchmarked Trans-NanoSim on direct RNA and complementary DNA datasets describing human and mouse transcriptomes. Through comparison against other nanopore read simulators, we show the unique advantage and robustness of Trans-NanoSim in capturing the characteristics of nanopore complementary DNA and direct RNA reads. As a cost-effective alternative to sequencing real transcriptomes, Trans-NanoSim will facilitate the rapid development of analytical tools for nanopore RNA-sequencing data. Trans-NanoSim and its pre-trained models are freely accessible at https://github.com/bcgsc/NanoSim.

| S-EPMC7285873 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data