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    94
  • Rank 356,972 (Top 8 %)
  • Language
    Python
  • License
    Other
  • Created over 7 years ago
  • Updated 2 months ago

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Repository Details

Analysis components from Oxford Nanopore Research

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1

dorado

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4

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
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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.
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6

fast-ctc-decode

Blitzing Fast CTC Beam Search Decoder
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7

remora

Methylation/modified base calling separated from basecalling.
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8

ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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9

modkit

A bioinformatics tool for working with modified bases
Rust
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10

pod5-file-format

Pod5: a high performance file format for nanopore reads.
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11

taiyaki

Training models for basecalling Oxford Nanopore reads
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12

pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
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113
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13

pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
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106
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14

read_until_api

Read Until client library for Nanopore Sequencing
Python
102
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15

rerio

Research release basecalling models and configurations
Python
102
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16

flappie

Flip-flop basecaller for Oxford Nanopore reads
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17

scrappie

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group
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18

ont-assembly-polish

ONT assembly and Illumina polishing pipeline
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19

pychopper

A tool to identify, orient, trim and rescue full length cDNA reads
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20

qcat

qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
Python
77
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21

jmespath-ts

Typescript translation of the jmespath.js package
TypeScript
63
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22

wub

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

minknow_api

Protobuf and gRPC specifications for the MinKNOW API
Python
55
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24

pore-c

Pore-C support
Python
53
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25

kmer_models

Predictive kmer models for development use
53
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26

katuali

Analysis pipelines from Oxford Nanopore Technologies' Research Division
Python
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27

duplex-tools

Splitting of sequence reads by internal adapter sequence search
Python
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28

pinfish

Tools to annotate genomes using long read transcriptomics data
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29

sockeye

Single Cell Transcriptomics
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30

vbz_compression

VBZ compression plugin for nanopore signal data
C++
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31

pipeline-nanopore-ref-isoforms

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

Pore-C-Snakemake

Python
33
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33

bwapy

Python bindings to bwa mem
Python
31
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34

ont_tutorial_basicqc

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

pyguppyclient

Python client library for Guppy
Python
30
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36

pipeline-umi-amplicon

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
Python
28
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37

pipeline-pinfish-analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish
Python
27
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38

pipeline-nanopore-denovo-isoforms

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

sloika

Sloika is Oxford Nanopore Technologies' software for training neural network models for base calling
Python
25
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40

fast5_research

Fast5 API provided by ONT Research
Python
21
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41

pyspoa

Python bindings to spoa
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18
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42

DTR-phage-pipeline

Python
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43

minimappy

Python bindings to minimap2
Python
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44

isONclust2

A tool for de novo clustering of long transcriptomic reads
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45

jmespath-plus

JMESPath with extended collection of built-in functions
TypeScript
14
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46

minknow_lims_interface

Protobuff and gRPC specifications for the MinKNOW LIMS Interface
13
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47

fast5mod

Extract modifed base call information from Guppy Fast5 files.
Python
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48

ont_h5_validator

Python
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49

dRNA-paper-scripts

Direct RNA publication scripts
Python
11
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50

currennt

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

pipeline-polya-diff

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

ont-open-datasets

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

pipeline-polya-ng

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

ts-runtime-typecheck

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

epi2me-api

API for communicating with the EPI2ME Platform for nanopore data analysis. Used by EPI2ME Agent & CLI.
TypeScript
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56

cronkite

One **hell** of a reporter
TypeScript
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57

mako

Analyte identification via squiggles.
Python
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58

marine-phage-paper-scripts

Python
6
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59

homebrew-tap

Homebrew casks for applications from Oxford Nanopore Technologies PLC and Metrichor Ltd.
Ruby
6
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60

barcoding

Naïve barcode deconvolution for amplicons
Perl
6
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61

ont-minimap2

Cross platform builds for minimap2
CMake
5
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62

plasmid-map

Plasmid map visualisations for Metrichor reports
TypeScript
5
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63

spliced_bam2gff

Go
5
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64

hammerpede

A package for training strand-specific profile HMMs for primer sets from real Nanopore data
Python
5
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65

hatch-protobuf

Hatch plugin for generating Python files from Protocol Buffers .proto files
Python
4
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66

fastq-filter

Quality and length filter for FastQ data
Python
4
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67

bripy

Bam Read Index for python
C
3
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68

pipeline-pychopper

Utility pipeline for running pychopper, a tool to identify full length cDNA reads
Python
3
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69

lamprey

GUI for desktop basecalling
JavaScript
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70

panga

Python
2
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71

data-rambler

An experimental language for a JSON query, transformation and streaming
TypeScript
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72

getopt-win32

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73

ts-argue

TypeScript
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74

onesie

A Linux device-driver for the MinION-mk1C
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75

vbz-h5py-plugin

Python
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76

fs-inspect

node.js library for indexing the contents of a folder
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