Discover nanoporetech/DTR-phage-pipeline 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

Splitting of sequence reads by internal adapter sequence search

duplex-tools

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

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