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Oxford Nanopore Technologies (@nanoporetech)

nanoporetech

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dorado

Oxford Nanopore's Basecaller

medaka

Sequence correction provided by ONT Research

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

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.

fast-ctc-decode

Blitzing Fast CTC Beam Search Decoder

remora

Methylation/modified base calling separated from basecalling.

ont_fast5_api

Oxford Nanopore Technologies fast5 API software

modkit

A bioinformatics tool for working with modified bases

pod5-file-format

Pod5: a high performance file format for nanopore reads.

taiyaki

Training models for basecalling Oxford Nanopore reads

pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

pipeline-transcriptome-de

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

read_until_api

Read Until client library for Nanopore Sequencing

rerio

Research release basecalling models and configurations

flappie

Flip-flop basecaller for Oxford Nanopore reads

pomoxis

Analysis components from Oxford Nanopore Research

scrappie

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group

ont-assembly-polish

ONT assembly and Illumina polishing pipeline

pychopper

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

qcat

qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.

jmespath-ts

Typescript translation of the jmespath.js package

wub

Tools and software library developed by the ONT Applications group

minknow_api

Protobuf and gRPC specifications for the MinKNOW API

pore-c

kmer_models

Predictive kmer models for development use

katuali

Analysis pipelines from Oxford Nanopore Technologies' Research Division

duplex-tools

Splitting of sequence reads by internal adapter sequence search

pinfish

Tools to annotate genomes using long read transcriptomics data

sockeye

Single Cell Transcriptomics

vbz_compression

VBZ compression plugin for nanopore signal data

pipeline-nanopore-ref-isoforms

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

Pore-C-Snakemake

bwapy

Python bindings to bwa mem

ont_tutorial_basicqc

A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt

pyguppyclient

Python client library for Guppy

pipeline-umi-amplicon

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers

pipeline-pinfish-analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish

pipeline-nanopore-denovo-isoforms

Pipeline for de novo clustering of long transcriptomic reads

sloika

Sloika is Oxford Nanopore Technologies' software for training neural network models for base calling

fast5_research

Fast5 API provided by ONT Research

pyspoa

Python bindings to spoa

DTR-phage-pipeline

minimappy

Python bindings to minimap2

isONclust2

A tool for de novo clustering of long transcriptomic reads

jmespath-plus

JMESPath with extended collection of built-in functions

minknow_lims_interface

Protobuff and gRPC specifications for the MinKNOW LIMS Interface

fast5mod

Extract modifed base call information from Guppy Fast5 files.

ont_h5_validator

dRNA-paper-scripts

Direct RNA publication scripts

currennt

Modified fork of CURRENNT https://sourceforge.net/projects/currennt/

pipeline-polya-diff

Pipeline for testing shifts in poly(A) tail lengths estimated by nanopolish

ont-open-datasets

Website describing data releases, and providing additional resources.

pipeline-polya-ng

Pipeline for calling poly(A) tail lengths from nanopore direct RNA data using nanopolish

ts-runtime-typecheck

A collection of common types for TypeScript along with dynamic type cast methods.

epi2me-api

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

cronkite

One **hell** of a reporter

mako

Analyte identification via squiggles.

marine-phage-paper-scripts

homebrew-tap

Homebrew casks for applications from Oxford Nanopore Technologies PLC and Metrichor Ltd.

barcoding

Naïve barcode deconvolution for amplicons

ont-minimap2

Cross platform builds for minimap2

plasmid-map

Plasmid map visualisations for Metrichor reports

spliced_bam2gff

hammerpede

A package for training strand-specific profile HMMs for primer sets from real Nanopore data

hatch-protobuf

Hatch plugin for generating Python files from Protocol Buffers .proto files

fastq-filter

Quality and length filter for FastQ data

bripy

Bam Read Index for python

pipeline-pychopper

Utility pipeline for running pychopper, a tool to identify full length cDNA reads

lamprey

GUI for desktop basecalling

panga

data-rambler

An experimental language for a JSON query, transformation and streaming

getopt-win32

ts-argue

onesie

A Linux device-driver for the MinION-mk1C

vbz-h5py-plugin

fs-inspect

node.js library for indexing the contents of a folder