basecalling

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…

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.

Cost-effective and scalable Oxford Nanopore Technologies (ONT) basecalling on AWS using Dorado, Nextflow, and AWS Batch with horizontal GPU scaling