basecalling
There are 21 repositories under basecalling topic.
nanoporetech/dorado
Oxford Nanopore's Basecaller
nanoporetech/bonito
A PyTorch Basecaller for Oxford Nanopore Reads
nanoporetech/megalodon
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.
nanoporetech/remora
Methylation/modified base calling separated from basecalling.
nanoporetech/rerio
Research release basecalling models and configurations
replikation/poreCov
SARS-CoV-2 workflow for nanopore sequence data
sirselim/guppy_parameter_optimiser
A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
nanoporetech/pyguppyclient
Python client library for Guppy
novoalab/modPhred
modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data
comprna/radian
Nanopore direct RNA basecaller
CMU-SAFARI/Molecules2Variations
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
vibaotram/baseDmux
snakemake workflow for basecalling and demultiplexing of ONT sequencing data
mbhall88/thesis
My PhD thesis
adamnapieralski/ravvent-basecaller
Novel basecaller, jointly processing raw and event data from ONT nanopore, basec on encoder-decoder + attention architecture
guangzhaocs/bioinformatics-starter
Quickstart to Bioinformatics & Biomedical AI.
shubhamchandak94/lossy_compression_evaluation
Impact of lossy compression of nanopore raw signal data on basecall and consensus accuracy
giesselmann/bumblebee
Nanopore Basecalling
quadram-institute-bioscience/dorado-gpu-testing
Benchmarking several NVIDIA GPUs with dorado
areebapatel/Rapid-CNS2
Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline
TJSanko/gridion_ont
Scripts for Basecalling on GridION Sequenicng machines from Oxford Nanopore
asadprodhan/Dorado-basecalled-reads-improve-old-bacterial-genome-assembly
Dorado-basecalled reads improve old bacterial genome assembly