basecalling

There are 0 repository under basecalling topic.

• nanoporetech / dorado

  Oxford Nanopore's Basecaller

  basecallinggenomicslibtorchnanopore
  Language:C++ 433

• nanoporetech / bonito

  A PyTorch Basecaller for Oxford Nanopore Reads

  basecallingnanoporepytorch
  Language:Python 380

• 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.

  basecallingepigeneticsguppyvariant-calling
  Language:Python 191

• nanoporetech / remora

  Methylation/modified base calling separated from basecalling.

  basecallingmethylationnanopore
  Language:Python 147

• nanoporetech / rerio

  Research release basecalling models and configurations

  basecallingnanopore
  Language:Python 96

• replikation / poreCov

  SARS-CoV-2 workflow for nanopore sequence data

  articbasecallingbioinformaticsnanoporenanopore-datasars-cov-2workflow
  Language:Nextflow 39

• sirselim / guppy_parameter_optimiser

  A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate

  guppybasecallinggpunanopore-sequencingoptimisation
  Language:Shell 31

• nanoporetech / pyguppyclient

  Python client library for Guppy

  basecallingpythonguppynanopore
  Language:Python 30

• novoalab / modPhred

  modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

  nanoporednarnafast5modificationsguppybasecallingon-the-fly
  Language:Python 15

• comprna / radian

  Nanopore direct RNA basecaller

  basecallingdeep-learninglanguage-modelnanoporerna
  Language:Python 10

• 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

  basecallingbioinformaticsfast5fastafastqgenome-analysishifiilluminaminimap2needleman-wunschquality-controlread-mappingsamsequence-alignmentsequencingsmith-watermanvariant-callingvcfwavefront-alignmentwfa
  8

• vibaotram / baseDmux

  snakemake workflow for basecalling and demultiplexing of ONT sequencing data

  snakemake-workflowbasecallingdemultiplexingnanopore
  Language:Python 6

• mbhall88 / thesis

  My PhD thesis

  bioinformaticsphd-thesisnanopore-sequencingtuberculosisbacterial-genomesgenome-graphsdrug-resistance-predictiontransmission-clusteringbasecalling
  Language:Jupyter Notebook 4

• adamnapieralski / ravvent-basecaller

  Novel basecaller, jointly processing raw and event data from ONT nanopore, basec on encoder-decoder + attention architecture

  sequence-to-sequencebasecallingencoder-decoderbioinformatics
  Language:Python 3

• guangzhaocs / bioinformatics-starter

  Quickstart to Bioinformatics & Biomedical AI.

  bioinformaticsnanoporenanopolishai4healthbasecalling
  Language:Python 3

• shubhamchandak94 / lossy_compression_evaluation

  Impact of lossy compression of nanopore raw signal data on basecall and consensus accuracy

  lossy-compressionnanopore-sequencingnanopore-analysis-pipelinebasecallingassemblyconsensus-algorithmmethylation-analysis
  Language:Jupyter Notebook 3

• giesselmann / bumblebee

  Nanopore Basecalling

  nanoporebasecalling
  Language:Python 1

• quadram-institute-bioscience / dorado-gpu-testing

  Benchmarking several NVIDIA GPUs with dorado

  basecallingdoradogpunanoporenvdia
  Language:Python 1

• areebapatel / Rapid-CNS2

  Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline

  nanopore-analysis-pipelinenanopore-sequencingbrain-tumor-classificationbrain-tumourssnakemake-workflowmethylationrapid-cns2variant-callingbasecallingmgmt
  Language:Shell 0

• TJSanko / gridion_ont

  Scripts for Basecalling on GridION Sequenicng machines from Oxford Nanopore

  basecallingbash-scriptbioinformatics-scriptsbioinformatics-toolgridionoxford-nanopore
  Language:Shell 0