Oxford Nanopore's Basecaller

A PyTorch Basecaller for Oxford Nanopore Reads

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

Methylation/modified base calling separated from basecalling.

Research release basecalling models and configurations

SARS-CoV-2 workflow for nanopore sequence data

Basecalling configuration prediction through FASTQ files

Python client library for Guppy

A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate

modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

Nanopore direct RNA basecaller

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https://arxiv.org/abs/2205.07957

Genomics for mobile hardware

snakemake workflow for basecalling and demultiplexing of ONT sequencing data

[NeurIPS 2024] A Multi-task Benchmark Dataset for Nanopore Sequencing.

My PhD thesis

A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.

Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline

Quickstart to Bioinformatics & Biomedical AI.

Novel basecaller, jointly processing raw and event data from ONT nanopore, basec on encoder-decoder + attention architecture

Nextflow pipeline for basecalling / demultiplexing ONT data, using Dorado

Impact of lossy compression of nanopore raw signal data on basecall and consensus accuracy

nanoRMS2 is a pipeline for detection of DNA/RNA modifications from raw ONT data

Nanopore Basecalling

Dorado-basecalled reads improve old bacterial genome assembly

Scripts for Basecalling on GridION Sequenicng machines from Oxford Nanopore

Docker container image for Slorado https://github.com/BonsonW/slorado

Nextflow pipeline to process ONT adaptive sampling runs (basecalling, mapping, statistics)

A performance analysis framework for neural network-based DNA basecalling from nanopore sequencing data. Implements and benchmarks LSTM and TCN architectures with CTC decoding, featuring comprehensive signal preprocessing pipelines and accuracy-speed tradeoff analysis for real-time genomic applications.