Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline
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Updated
May 27, 2022 - Shell
Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline
Scripts for Basecalling on GridION Sequenicng machines from Oxford Nanopore
Benchmarking several NVIDIA GPUs with dorado
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
Quickstart to Bioinformatics & Biomedical AI.
My PhD thesis
snakemake workflow for basecalling and demultiplexing of ONT sequencing data
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…
Nanopore direct RNA basecaller
modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data
A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
SARS-CoV-2 workflow for nanopore sequence data
Research release basecalling models and configurations
Methylation/modified base calling separated from basecalling.
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.
A PyTorch Basecaller for Oxford Nanopore Reads
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