Oxford Nanopore Technologies

Repositories

• 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.

  epigenetics variant-calling basecalling guppy
  Python 8 66 3 0 Updated Nov 9, 2020

• Pore-C-Snakemake
  Python 3 6 6 1 Updated Nov 9, 2020

• pipeline-nanopore-denovo-isoforms

  Pipeline for de novo clustering of long transcriptomic reads

  rna-seq rna transcriptomics cdna
  Python 0 10 2 0 Updated Nov 9, 2020

• medaka

  Sequence correction provided by ONT Research

  nanopore medaka
  Python MPL-2.0 29 137 12 1 Updated Nov 6, 2020

• pipeline-umi-amplicon

  Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
  Python 0 2 1 0 Updated Nov 5, 2020

• jmespath-ts

  Typescript translation of the jmespath.js package
  TypeScript MPL-2.0 1 13 0 0 Updated Nov 3, 2020

• ts-extended-types

  A collection of common types for TypeScript along with dynamic type cast methods.
  TypeScript 0 1 0 0 Updated Nov 3, 2020

• fast5mod

  Extract modifed base call information from Guppy Fast5 files.
  Python 1 5 4 0 Updated Nov 2, 2020

• bonito

  Bonito - A PyTorch Basecaller for Oxford Nanopore Reads

  nanopore pytorch basecalling
  Python 25 93 12 1 Updated Nov 2, 2020

• read_until_api

  Read Until client library for Nanopore Sequencing
  Python 7 46 0 0 Updated Oct 30, 2020

• ont-open-datasets

  Website describing data releases, and providing additional resources.
  JavaScript 1 5 0 0 Updated Oct 30, 2020

• pipeline-transcriptome-de

  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

  rna-seq nanopore differential-gene-expression cdna differential-transcript-usage
  Python 8 55 7 0 Updated Oct 27, 2020

• pipeline-nanopore-ref-isoforms

  Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools

  rna-seq rna-seq-analysis cdna nanopore-sequencing
  Python 1 8 4 1 Updated Oct 26, 2020

• pychopper

  A tool to identify, orient, trim and rescue full length cDNA reads

  rna-seq nanopore transcriptomics cdna full-length
  Python 13 40 4 0 Updated Oct 22, 2020

• cronkite

  One **hell** of a reporter

  web-components dashboard-widget dashboards dashboard-application dashboard-framework stenciljs stencil-components
  TypeScript MPL-2.0 1 6 0 0 Updated Oct 20, 2020

• jmespath-plus

  JMESPath with extended collection of built-in functions
  TypeScript MPL-2.0 1 2 0 0 Updated Oct 17, 2020

• katuali

  Analysis pipelines from Oxford Nanopore Technologies' Research Division
  Python 4 33 3 0 Updated Oct 16, 2020

• rerio

  Research release basecalling models and configurations

  nanopore basecalling
  Python 2 14 1 0 Updated Oct 15, 2020

• panga
  Python MPL-2.0 1 1 1 0 Updated Oct 13, 2020

• qcat

  qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
  Python MPL-2.0 10 61 24 2 Updated Oct 13, 2020

• pyspoa

  Python bindings to spoa

  nanopore alignment poa multiple-sequence-alignment
  Python MIT 0 3 0 0 Updated Oct 4, 2020

• open-data-registry

  Forked from awslabs/open-data-registry

  A registry of publicly available datasets on AWS
  Python Apache-2.0 362 1 0 0 Updated Sep 29, 2020

• epi2me-api

  API for communicating with the EPI2ME Platform for nanopore data analysis. Used by EPI2ME Agent & CLI.

  bioinformatics nanopore epi2me metrichor minknow
  JavaScript MPL-2.0 1 1 2 0 Updated Sep 28, 2020

• homebrew-tap
  Ruby 0 1 0 0 Updated Sep 9, 2020

• kmer_models

  Predictive kmer models for development use
  MPL-2.0 6 13 0 0 Updated Sep 7, 2020

• fast5_research

  Fast5 API provided by ONT Research
  Python 10 18 0 0 Updated Aug 25, 2020

• DTR-phage-pipeline
  Python MPL-2.0 5 5 1 0 Updated Aug 24, 2020

• ont_fast5_api

  Oxford Nanopore Technologies fast5 API software
  Python MPL-2.0 21 68 5 0 Updated Aug 20, 2020

• ont_minimap2
  C++ 2 3 0 0 Updated Jul 24, 2020

• minknow_api

  Protobuff and gRPC specifications for the MinKNOW API
  Python 2 10 1 0 Updated Jul 13, 2020