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

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

Python client library for Guppy

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…

snakemake workflow for basecalling and demultiplexing of ONT sequencing data

My PhD thesis

Quickstart to Bioinformatics & Biomedical AI.

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

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

Nanopore Basecalling

Benchmarking several NVIDIA GPUs with dorado

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

Nextflow pipeline for basecalling / demultiplexing ONT data, using Dorado