Discover nanoporetech/duplex-tools Open Source project

Sequence correction provided by ONT Research

493

medaka

A PyTorch Basecaller for Oxford Nanopore Reads

411

bonito

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

392

tombo

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.

230

megalodon

Blitzing Fast CTC Beam Search Decoder

197

fast-ctc-decode

Rust

176

remora

Methylation/modified base calling separated from basecalling.

Oxford Nanopore Technologies fast5 API software

156

ont_fast5_api

A bioinformatics tool for working with modified bases

146

modkit

Rust

137

pod5-file-format

Pod5: a high performance file format for nanopore reads.

Training models for basecalling Oxford Nanopore reads

131

taiyaki

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

114

pipeline-structural-variation

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

113

pipeline-transcriptome-de

Read Until client library for Nanopore Sequencing

106

read_until_api

Research release basecalling models and configurations

102

rerio

Flip-flop basecaller for Oxford Nanopore reads

102

flappie

pomoxis

Analysis components from Oxford Nanopore Research

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

scrappie

ont-assembly-polish

ONT assembly and Illumina polishing pipeline

Makefile

pychopper

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

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

qcat

Typescript translation of the jmespath.js package

jmespath-ts

Tools and software library developed by the ONT Applications group

wub

Protobuf and gRPC specifications for the MinKNOW API

minknow_api

pore-c

Pore-C support

Predictive kmer models for development use

kmer_models

katuali

Analysis pipelines from Oxford Nanopore Technologies' Research Division

Tools to annotate genomes using long read transcriptomics data

pinfish

sockeye

Single Cell Transcriptomics

VBZ compression plugin for nanopore signal data

vbz_compression

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

pipeline-nanopore-ref-isoforms

Pore-C-Snakemake

Python bindings to bwa mem

bwapy

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

ont_tutorial_basicqc

TeX

pyguppyclient

Python client library for Guppy

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

pipeline-umi-amplicon

Pipeline for annotating genomes using long read transcriptomics data with pinfish

pipeline-pinfish-analysis

Pipeline for de novo clustering of long transcriptomic reads

pipeline-nanopore-denovo-isoforms

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

sloika

Fast5 API provided by ONT Research

fast5_research

pyspoa

Python bindings to spoa

DTR-phage-pipeline

Python bindings to minimap2

minimappy

A tool for de novo clustering of long transcriptomic reads

isONclust2

JMESPath with extended collection of built-in functions

jmespath-plus

Protobuff and gRPC specifications for the MinKNOW LIMS Interface

minknow_lims_interface

fast5mod

Extract modifed base call information from Guppy Fast5 files.

ont_h5_validator

Direct RNA publication scripts

dRNA-paper-scripts

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

currennt

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

pipeline-polya-diff

Website describing data releases, and providing additional resources.

ont-open-datasets

HTML

pipeline-polya-ng

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

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

ts-runtime-typecheck

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

epi2me-api

One **hell** of a reporter

cronkite

Analyte identification via squiggles.

mako

marine-phage-paper-scripts

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

homebrew-tap

Ruby

barcoding

Naïve barcode deconvolution for amplicons

Perl

ont-minimap2

Cross platform builds for minimap2

CMake

plasmid-map

Plasmid map visualisations for Metrichor reports

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

spliced_bam2gff

hammerpede

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

hatch-protobuf

Quality and length filter for FastQ data

fastq-filter

Bam Read Index for python

bripy

pipeline-pychopper

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

GUI for desktop basecalling

lamprey

JavaScript

panga

An experimental language for a JSON query, transformation and streaming

data-rambler

getopt-win32

ts-argue

A Linux device-driver for the MinION-mk1C

onesie

vbz-h5py-plugin

node.js library for indexing the contents of a folder

fs-inspect