Oxford Nanopore Technologies (@nanoporetech)
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nanoporetech

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Top repositories

1

medaka

Sequence correction provided by ONT Research
Python
380
star
2

bonito

A PyTorch Basecaller for Oxford Nanopore Reads
Python
372
star
3

dorado

Oxford Nanopore's Basecaller
C++
369
star
4

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
Python
220
star
5

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.
Python
189
star
6

fast-ctc-decode

Blitzing Fast CTC Beam Search Decoder
Rust
174
star
7

ont_fast5_api

Oxford Nanopore Technologies fast5 API software
Python
141
star
8

remora

Methylation/modified base calling separated from basecalling.
Python
138
star
9

taiyaki

Training models for basecalling Oxford Nanopore reads
Python
111
star
10

pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
Python
111
star
11

pod5-file-format

Pod5: a high performance file format for nanopore reads.
C++
108
star
12

pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
Python
105
star
13

read_until_api

Read Until client library for Nanopore Sequencing
Python
101
star
14

modkit

A bioinformatics tool for working with modified bases
Rust
99
star
15

flappie

Flip-flop basecaller for Oxford Nanopore reads
C
98
star
16

ont-assembly-polish

ONT assembly and Illumina polishing pipeline
Makefile
90
star
17

rerio

Research release basecalling models and configurations
Python
89
star
18

scrappie

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group
C
88
star
19

pomoxis

Analysis components from Oxford Nanopore Research
Python
85
star
20

qcat

qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
Python
78
star
21

pychopper

A tool to identify, orient, trim and rescue full length cDNA reads
Python
77
star
22

wub

Tools and software library developed by the ONT Applications group
Python
61
star
23

pore-c

Pore-C support
Python
51
star
24

minknow_api

Protobuf and gRPC specifications for the MinKNOW API
Python
50
star
25

kmer_models

Predictive kmer models for development use
50
star
26

katuali

Analysis pipelines from Oxford Nanopore Technologies' Research Division
Python
50
star
27

jmespath-ts

Typescript translation of the jmespath.js package
TypeScript
49
star
28

duplex-tools

Splitting of sequence reads by internal adapter sequence search
Python
47
star
29

pinfish

Tools to annotate genomes using long read transcriptomics data
Go
43
star
30

sockeye

Single Cell Transcriptomics
Python
40
star
31

pipeline-nanopore-ref-isoforms

Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools
Python
36
star
32

Pore-C-Snakemake

Python
33
star
33

bwapy

Python bindings to bwa mem
Python
30
star
34

ont_tutorial_basicqc

A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt
TeX
30
star
35

pyguppyclient

Python client library for Guppy
Python
30
star
36

pipeline-pinfish-analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish
Python
27
star
37

pipeline-umi-amplicon

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
Python
26
star
38

pipeline-nanopore-denovo-isoforms

Pipeline for de novo clustering of long transcriptomic reads
Python
26
star
39

sloika

Sloika is Oxford Nanopore Technologies' software for training neural network models for base calling
Python
24
star
40

fast5_research

Fast5 API provided by ONT Research
Python
20
star
41

DTR-phage-pipeline

Python
16
star
42

minimappy

Python bindings to minimap2
Python
16
star
43

jmespath-plus

JMESPath with extended collection of built-in functions
TypeScript
14
star
44

minknow_lims_interface

Protobuff and gRPC specifications for the MinKNOW LIMS Interface
13
star
45

isONclust2

A tool for de novo clustering of long transcriptomic reads
C++
13
star
46

ont_h5_validator

Python
12
star
47

pyspoa

Python bindings to spoa
Python
12
star
48

fast5mod

Extract modifed base call information from Guppy Fast5 files.
Python
12
star
49

dRNA-paper-scripts

Direct RNA publication scripts
Python
11
star
50

currennt

Modified fork of CURRENNT https://sourceforge.net/projects/currennt/
C++
11
star
51

pipeline-polya-diff

Pipeline for testing shifts in poly(A) tail lengths estimated by nanopolish
Python
9
star
52

ont-open-datasets

Website describing data releases, and providing additional resources.
HTML
9
star
53

pipeline-polya-ng

Pipeline for calling poly(A) tail lengths from nanopore direct RNA data using nanopolish
Python
9
star
54

ts-runtime-typecheck

A collection of common types for TypeScript along with dynamic type cast methods.
TypeScript
9
star
55

cronkite

One **hell** of a reporter
TypeScript
8
star
56

epi2me-api

API for communicating with the EPI2ME Platform for nanopore data analysis. Used by EPI2ME Agent & CLI.
TypeScript
8
star
57

mako

Analyte identification via squiggles.
Python
7
star
58

marine-phage-paper-scripts

Python
6
star
59

barcoding

Naïve barcode deconvolution for amplicons
Perl
6
star
60

ont-minimap2

Cross platform builds for minimap2
CMake
5
star
61

plasmid-map

Plasmid map visualisations for Metrichor reports
TypeScript
5
star
62

hammerpede

A package for training strand-specific profile HMMs for primer sets from real Nanopore data
Python
5
star
63

spliced_bam2gff

Go
4
star
64

homebrew-tap

Homebrew casks for applications from Oxford Nanopore Technologies PLC and Metrichor Ltd.
Ruby
4
star
65

fastq-filter

Quality and length filter for FastQ data
Python
4
star
66

bripy

Bam Read Index for python
C
3
star
67

lamprey

GUI for desktop basecalling
JavaScript
3
star
68

panga

Python
2
star
69

data-rambler

An experimental language for a JSON query, transformation and streaming
TypeScript
2
star
70

pipeline-pychopper

Utility pipeline for running pychopper, a tool to identify full length cDNA reads
Python
2
star
71

getopt-win32

C
2
star
72

ts-argue

TypeScript
1
star
73

onesie

A Linux device-driver for the MinION-mk1C
C
1
star
74

vbz-h5py-plugin

Python
1
star
75

fs-inspect

node.js library for indexing the contents of a folder
TypeScript
1
star