Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: basecalling
guangzhaocs/bioinformatics-starter
Quickstart to Bioinformatics & Biomedical AI.
Language: Python - Size: 282 KB - Last synced: about 21 hours ago - Pushed: about 22 hours ago - Stars: 3 - Forks: 0
replikation/poreCov
SARS-CoV-2 workflow for nanopore sequence data
Language: Nextflow - Size: 28.4 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 39 - Forks: 15
nanoporetech/dorado
Oxford Nanopore's Basecaller
Language: C++ - Size: 14.2 MB - Last synced: 6 days ago - Pushed: 10 days ago - Stars: 395 - Forks: 51
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.
Language: Python - Size: 24.9 MB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 190 - Forks: 29
nanoporetech/bonito
A PyTorch Basecaller for Oxford Nanopore Reads
Language: Python - Size: 745 KB - Last synced: 6 days ago - Pushed: 5 months ago - Stars: 374 - Forks: 116
nanoporetech/rerio
Research release basecalling models and configurations
Language: Python - Size: 114 KB - Last synced: 10 days ago - Pushed: 5 months ago - Stars: 90 - Forks: 9
novoalab/modPhred
modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data
Language: Python - Size: 47.9 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 13 - Forks: 1
nanoporetech/remora
Methylation/modified base calling separated from basecalling.
Language: Python - Size: 44.5 MB - Last synced: 25 days ago - Pushed: 2 months ago - Stars: 139 - Forks: 17
quadram-institute-bioscience/dorado-gpu-testing Fork of thanhleviet/dorado-gpu-testing
Benchmarking several NVIDIA GPUs with dorado
Language: Python - Size: 445 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0
areebapatel/Rapid-CNS2 📦
Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline
Language: Shell - Size: 572 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
sirselim/guppy_parameter_optimiser
A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
Language: Shell - Size: 46.9 KB - Last synced: 4 months ago - Pushed: about 2 years ago - Stars: 31 - Forks: 4
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
Size: 4.31 MB - Last synced: 23 days ago - Pushed: almost 2 years ago - Stars: 8 - Forks: 0
nanoporetech/pyguppyclient 📦
Python client library for Guppy
Language: Python - Size: 93.8 KB - Last synced: 25 days ago - Pushed: almost 2 years ago - Stars: 30 - Forks: 5
adamnapieralski/ravvent-basecaller
Novel basecaller, jointly processing raw and event data from ONT nanopore, basec on encoder-decoder + attention architecture
Language: Python - Size: 4.77 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 1
mbhall88/thesis
My PhD thesis
Language: Jupyter Notebook - Size: 57 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 4 - Forks: 0
mbhall88/tubby-manuscript
Manuscript for our work training and evaluating a Mycobacterium tuberculosis-specific Nanopore basecalling model
Language: HTML - Size: 876 KB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
vibaotram/baseDmux
snakemake workflow for basecalling and demultiplexing of ONT sequencing data
Language: Python - Size: 84.2 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 4 - Forks: 1
comprna/radian
Nanopore direct RNA basecaller
Language: Python - Size: 70.9 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 6 - Forks: 2
shubhamchandak94/lossy_compression_evaluation
Impact of lossy compression of nanopore raw signal data on basecall and consensus accuracy
Language: Jupyter Notebook - Size: 254 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 3 - Forks: 0
giesselmann/bumblebee
Nanopore Basecalling
Language: Python - Size: 966 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0
