Quickstart to Bioinformatics & Biomedical AI.
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Updated
Jun 26, 2024 - Python
Quickstart to Bioinformatics & Biomedical AI.
Research release basecalling models and configurations
A PyTorch Basecaller for Oxford Nanopore Reads
Dorado-basecalled reads improve old bacterial genome assembly
Methylation/modified base calling separated from basecalling.
SARS-CoV-2 workflow for nanopore sequence data
modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data
Benchmarking several NVIDIA GPUs with dorado
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.
snakemake workflow for basecalling and demultiplexing of ONT sequencing data
Nanopore direct RNA basecaller
Scripts for Basecalling on GridION Sequenicng machines from Oxford Nanopore
Novel basecaller, jointly processing raw and event data from ONT nanopore, basec on encoder-decoder + attention architecture
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…
Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline
A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
My PhD thesis
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