ArticleBioinformatics (Oxford, England)2017
Nanocall: an open source basecaller for Oxford Nanopore sequencing data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.
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Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
- BRCA genes as candidates for colorectal cancer genetic testing panel: systematic review and meta-analysis.BMC cancer · 2023Pooled it
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- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.Bioinformatics (Oxford, England) · 2026Article
- Bream: an open-source deep learning framework for simultaneous base calling and DNA methylation detection on novel nanopore sequencing platforms.Frontiers in genetics · 2026Article
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- Nanopore-Aware Embedded Detection for Mobile DNA Sequencing: A Viterbi-HMM Design Versus Deep Learning Approaches.Biosensors · 2025Article
- Brownian motion data augmentation: a method to push neural network performance on nanopore sensors.Bioinformatics (Oxford, England) · 2025Article
- ReQuant: improved base modification calling by k-mer value imputation.Nucleic acids research · 2025Article
- Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment.Nature methods · 2025Article
- SqueezeCall: nanopore basecalling using a Squeezeformer network.GigaByte (Hong Kong, China) · 2025Article
- BaseNet: A transformer-based toolkit for nanopore sequencing signal decoding.Computational and structural biotechnology journal · 2024Article
- Single-Molecule Bioelectronic Sensors with AI-Aided Data Analysis: Convergence and Challenges.Precision chemistry · 2024Review
- A generalized protein identification method for novel and diverse sequencing technologies.NAR genomics and bioinformatics · 2024Article
- Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics.Nature chemistry · 2024Review
- GCRTcall: a transformer based basecaller for nanopore RNA sequencing enhanced by gated convolution and relative position embedding via joint loss training.Frontiers in genetics · 2024Article
- Solid-State Nanopores for Biomolecular Analysis and Detection.Advances in biochemical engineering/biotechnology · 2024Review
- Estimated Nucleotide Reconstruction Quality Symbols of Basecalling Tools for Oxford Nanopore Sequencing.Sensors (Basel, Switzerland) · 2023Article
- RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes.Bioinformatics (Oxford, England) · 2023Article
- Genome Organization of Four Brazilian Xanthomonas albilineans Strains Does Not Correlate with Aggressiveness.Microbiology spectrum · 2023Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationThe highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls.
resultsTo allow offline and private analysis of MinION data, we created Nanocall. Nanocall is the first freely available, open-source basecaller for Oxford Nanopore sequencing data and does not require an internet connection. Using R7.3 chemistry, on two E.coli and two human samples, with natural as well as PCR-amplified DNA, Nanocall reads have ∼68% identity, directly comparable to Metrichor '1D' data. Further, Nanocall is efficient, processing ∼2500 Kbp of sequence per core hour using the fastest settings, and fully parallelized. Using a 4 core desktop computer, Nanocall could basecall a MinION sequencing run in real time. Metrichor provides the ability to integrate the '1D' sequencing of template and complement strands of a single DNA molecule, and create a '2D' read. Nanocall does not currently integrate this technology, and addition of this capability will be an important future development. In summary, Nanocall is the first open-source, freely available, off-line basecaller for Oxford Nanopore sequencing data. AVAILABILITY AND IMPLEMENTATION: Nanocall is available at github.com/mateidavid/nanocall, released under the MIT license. CONTACT: matei.david@oicr.on.caSupplementary information: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.