nanoporetech/dorado

Oxford Nanopore's Basecaller

Language: C++ - Size: 23.4 MB - Last synced at: about 3 hours ago - Pushed at: about 2 months ago - Stars: 694 - Forks: 89

nanoporetech/jmespath-plus

JMESPath with extended collection of built-in functions

Language: TypeScript - Size: 675 KB - Last synced at: 8 days ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 0

nanoporetech/medaka

Sequence correction provided by ONT Research

Language: Python - Size: 94.8 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 466 - Forks: 84

nanoporetech/hatch-protobuf

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

Language: Python - Size: 41 KB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 8 - Forks: 3

nanoporetech/modkit

A bioinformatics tool for working with modified bases

Language: Rust - Size: 205 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 204 - Forks: 15

nanoporetech/pomfret

Language: C - Size: 6.57 MB - Last synced at: 11 days ago - Pushed at: 12 days ago - Stars: 20 - Forks: 0

nanoporetech/pod5-file-format

Pod5: a high performance file format for nanopore reads.

Language: C++ - Size: 29 MB - Last synced at: 10 days ago - Pushed at: 2 months ago - Stars: 152 - Forks: 21

nanoporetech/ont-spectre

Language: Python - Size: 80.1 MB - Last synced at: 8 days ago - Pushed at: 3 months ago - Stars: 10 - Forks: 2

nanoporetech/bonito

A PyTorch Basecaller for Oxford Nanopore Reads

Language: Python - Size: 771 KB - Last synced at: 28 days ago - Pushed at: about 1 month ago - Stars: 420 - Forks: 125

nanoporetech/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.

Language: Python - Size: 24.9 MB - Last synced at: 27 days ago - Pushed at: about 2 years ago - Stars: 202 - Forks: 27

nanoporetech/remora

Methylation/modified base calling separated from basecalling.

Language: Python - Size: 45 MB - Last synced at: 25 days ago - Pushed at: 10 months ago - Stars: 176 - Forks: 22

nanoporetech/fast5mod 📦

Extract modifed base call information from Guppy Fast5 files.

Language: Python - Size: 95.7 KB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 14 - Forks: 3

nanoporetech/dorado-docs

Dorado Documentation

Language: Python - Size: 319 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 0

nanoporetech/ont-output-specifications

Specifications for output files from MinKNOW, dorado and others

Language: Python - Size: 1.23 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

nanoporetech/fast5_research

Fast5 API provided by ONT Research

Language: Python - Size: 15.3 MB - Last synced at: 25 days ago - Pushed at: over 3 years ago - Stars: 22 - Forks: 15

nanoporetech/minknow_api

Protobuf and gRPC specifications for the MinKNOW API

Language: Python - Size: 2.35 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 64 - Forks: 13

nanoporetech/rerio

Research release basecalling models and configurations

Language: Python - Size: 124 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 110 - Forks: 10

nanoporetech/epi2me-api

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

Language: TypeScript - Size: 61.4 MB - Last synced at: 8 days ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 8

nanoporetech/fast-ctc-decode

Blitzing Fast CTC Beam Search Decoder

Language: Rust - Size: 307 KB - Last synced at: 28 days ago - Pushed at: about 1 year ago - Stars: 183 - Forks: 27

nanoporetech/duplex-tools

Splitting of sequence reads by internal adapter sequence search

Language: Python - Size: 23.6 MB - Last synced at: 10 days ago - Pushed at: about 2 years ago - Stars: 51 - Forks: 8

nanoporetech/ont_fast5_api

Oxford Nanopore Technologies fast5 API software

Language: Python - Size: 4.02 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 154 - Forks: 30

nanoporetech/vbz_compression

VBZ compression plugin for nanopore signal data

Language: C++ - Size: 3.87 MB - Last synced at: 14 days ago - Pushed at: 4 months ago - Stars: 40 - Forks: 10

nanoporetech/pyspoa

Python bindings to spoa

Language: Python - Size: 45.9 KB - Last synced at: 10 days ago - Pushed at: almost 2 years ago - Stars: 20 - Forks: 3

nanoporetech/qcat 📦

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

Language: Python - Size: 7.87 MB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 79 - Forks: 17

nanoporetech/jmespath-ts

Typescript translation of the jmespath.js package

Language: TypeScript - Size: 641 KB - Last synced at: 20 days ago - Pushed at: over 2 years ago - Stars: 69 - Forks: 7

nanoporetech/ont-minimap2

Cross platform builds for minimap2

Language: CMake - Size: 46.9 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 6 - Forks: 2

nanoporetech/tombo

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

Language: Python - Size: 37.8 MB - Last synced at: 28 days ago - Pushed at: about 2 years ago - Stars: 233 - Forks: 54

nanoporetech/read_until_api

Read Until client library for Nanopore Sequencing

Language: Python - Size: 707 KB - Last synced at: 3 months ago - Pushed at: 10 months ago - Stars: 104 - Forks: 13

nanoporetech/pipeline-transcriptome-de 📦

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

Language: Python - Size: 124 KB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 108 - Forks: 26

nanoporetech/pipeline-pinfish-analysis 📦

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Language: Python - Size: 137 KB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 27 - Forks: 5

nanoporetech/fs-inspect

node.js library for indexing the contents of a folder

Language: TypeScript - Size: 354 KB - Last synced at: 8 days ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

nanoporetech/isONclust2

A tool for de novo clustering of long transcriptomic reads

Language: C++ - Size: 643 KB - Last synced at: 4 months ago - Pushed at: almost 3 years ago - Stars: 15 - Forks: 3

nanoporetech/scrappie 📦

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

Language: C - Size: 69.3 MB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 93 - Forks: 27

nanoporetech/pipeline-polya-diff

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

Language: Python - Size: 45.9 KB - Last synced at: about 2 months ago - Pushed at: about 5 years ago - Stars: 11 - Forks: 4

nanoporetech/pipeline-umi-amplicon

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

Language: Python - Size: 201 KB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 33 - Forks: 11

nanoporetech/pyguppyclient 📦

Python client library for Guppy

Language: Python - Size: 93.8 KB - Last synced at: 4 days ago - Pushed at: almost 3 years ago - Stars: 31 - Forks: 6

nanoporetech/homebrew-tap

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

Language: Ruby - Size: 221 KB - Last synced at: 4 months ago - Pushed at: 7 months ago - Stars: 6 - Forks: 0

nanoporetech/nanopolish Fork of jts/nanopolish

Signal-level algorithms for MinION data

Language: C++ - Size: 8.55 MB - Last synced at: 4 months ago - Pushed at: almost 6 years ago - Stars: 9 - Forks: 1

nanoporetech/bripy

Bam Read Index for python

Language: C - Size: 140 KB - Last synced at: about 1 month ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 0

nanoporetech/kmer_models

Predictive kmer models for development use

Size: 8.9 MB - Last synced at: 4 months ago - Pushed at: about 2 years ago - Stars: 54 - Forks: 19

nanoporetech/bwapy

Python bindings to bwa mem

Language: Python - Size: 5.97 MB - Last synced at: 4 months ago - Pushed at: over 5 years ago - Stars: 32 - Forks: 12

nanoporetech/pychopper 📦

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

Language: Python - Size: 52 MB - Last synced at: 4 months ago - Pushed at: about 3 years ago - Stars: 81 - Forks: 22

nanoporetech/wub 📦

Tools and software library developed by the ONT Applications group

Language: Python - Size: 385 KB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 62 - Forks: 10

nanoporetech/pipeline-structural-variation 📦

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

Language: Python - Size: 6.22 MB - Last synced at: 4 months ago - Pushed at: almost 4 years ago - Stars: 114 - Forks: 17

nanoporetech/pomoxis

Analysis components from Oxford Nanopore Research

Language: Python - Size: 4.86 MB - Last synced at: 29 days ago - Pushed at: 11 months ago - Stars: 93 - Forks: 23

nanoporetech/plasmid-map

Plasmid map visualisations for Metrichor reports

Language: TypeScript - Size: 663 KB - Last synced at: 14 days ago - Pushed at: about 3 years ago - Stars: 6 - Forks: 2

nanoporetech/taiyaki 📦

Training models for basecalling Oxford Nanopore reads

Language: Python - Size: 53.5 MB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 115 - Forks: 43

nanoporetech/flappie 📦

Flip-flop basecaller for Oxford Nanopore reads

Language: C - Size: 8.12 MB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 99 - Forks: 15

nanoporetech/pipeline-polya-ng

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

Language: Python - Size: 49.8 KB - Last synced at: 4 months ago - Pushed at: about 5 years ago - Stars: 10 - Forks: 2

nanoporetech/pore-c 📦

Pore-C support

Language: Python - Size: 2.3 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 53 - Forks: 6

nanoporetech/pinfish 📦

Tools to annotate genomes using long read transcriptomics data

Language: Go - Size: 120 MB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 45 - Forks: 13

nanoporetech/Pore-C-Snakemake 📦

Language: Python - Size: 1.91 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 33 - Forks: 15

nanoporetech/spliced_bam2gff

Language: Go - Size: 16 MB - Last synced at: 4 months ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 2

nanoporetech/ont-assembly-polish 📦

ONT assembly and Illumina polishing pipeline

Language: Makefile - Size: 1.2 MB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 91 - Forks: 18

nanoporetech/onesie

A Linux device-driver for the MinION-mk1C

Language: C - Size: 601 KB - Last synced at: 4 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

nanoporetech/pipeline-pychopper 📦

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

Language: Python - Size: 70.3 KB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0

nanoporetech/Clair3 Fork of HKU-BAL/Clair3

Clair3 - Integrating pileup and full-alignment for high-performance long-read variant calling

Language: Python - Size: 1.65 MB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 1

nanoporetech/sloika 📦

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

Language: Python - Size: 6 MB - Last synced at: 4 months ago - Pushed at: almost 3 years ago - Stars: 25 - Forks: 7

nanoporetech/sqlpad Fork of sqlpad/sqlpad

Web-based SQL editor run in your own private cloud. Supports MySQL, Postgres, SQL Server, Vertica, Crate, ClickHouse, Trino, Presto, SAP HANA, Cassandra, Snowflake, BigQuery, SQLite, and more with ODBC

Language: JavaScript - Size: 31.6 MB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

nanoporetech/sockeye 📦

Single Cell Transcriptomics

Language: Python - Size: 51.8 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 39 - Forks: 10

nanoporetech/katuali

Analysis pipelines from Oxford Nanopore Technologies' Research Division

Language: Python - Size: 33.4 MB - Last synced at: about 1 month ago - Pushed at: almost 5 years ago - Stars: 50 - Forks: 7

nanoporetech/panga

Language: Python - Size: 7.39 MB - Last synced at: 4 months ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 1

nanoporetech/DTR-phage-pipeline

Language: Python - Size: 10.7 MB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 6

nanoporetech/vbz-h5py-plugin

Language: Python - Size: 3.13 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

nanoporetech/dRNA-paper-scripts

Direct RNA publication scripts

Language: Python - Size: 8.79 KB - Last synced at: 4 months ago - Pushed at: almost 8 years ago - Stars: 11 - Forks: 1

nanoporetech/ont_tutorial_basicqc 📦

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

Language: TeX - Size: 95.4 MB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 30 - Forks: 14

nanoporetech/tfjs Fork of tensorflow/tfjs

A WebGL accelerated JavaScript library for training and deploying ML models.

Language: TypeScript - Size: 132 MB - Last synced at: 30 days ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

nanoporetech/lamprey 📦

GUI for desktop basecalling

Language: JavaScript - Size: 5.23 MB - Last synced at: 4 months ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 0

nanoporetech/minknow_lims_interface 📦

Protobuff and gRPC specifications for the MinKNOW LIMS Interface

Size: 154 KB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 13 - Forks: 4

nanoporetech/ont-open-datasets

Website describing data releases, and providing additional resources.

Language: HTML - Size: 6.78 MB - Last synced at: 4 months ago - Pushed at: about 4 years ago - Stars: 9 - Forks: 3

nanoporetech/pipeline-nanopore-denovo-isoforms 📦

Pipeline for de novo clustering of long transcriptomic reads

Language: Python - Size: 27.2 MB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 26 - Forks: 6

nanoporetech/ont_h5_validator

Language: Python - Size: 57.6 KB - Last synced at: 4 months ago - Pushed at: almost 7 years ago - Stars: 12 - Forks: 2

nanoporetech/lc23-poster-avian-flu

Size: 59.6 KB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

nanoporetech/data-rambler

An experimental language for a JSON query, transformation and streaming

Language: TypeScript - Size: 698 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

nanoporetech/currennt 📦

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

Language: C++ - Size: 97.3 MB - Last synced at: 4 months ago - Pushed at: almost 9 years ago - Stars: 11 - Forks: 5

nanoporetech/linux-minit-nvidia

ONT modified git://nv-tegra.nvidia.com/linux-nvidia.git.

Language: C - Size: 63.6 MB - Last synced at: 4 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

nanoporetech/ts-argue

Language: TypeScript - Size: 1.24 MB - Last synced at: 16 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

nanoporetech/ts-runtime-typecheck

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

Language: TypeScript - Size: 392 KB - Last synced at: 5 days ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 0

nanoporetech/cronkite

One **hell** of a reporter

Language: TypeScript - Size: 4.19 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 0

nanoporetech/minimappy

Python bindings to minimap2

Language: Python - Size: 1.44 MB - Last synced at: 4 months ago - Pushed at: almost 8 years ago - Stars: 16 - Forks: 1

nanoporetech/vbz_js

JS bindings for VBZ compression

Language: WebAssembly - Size: 3.27 MB - Last synced at: 19 days ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

nanoporetech/yellowfin Fork of ubuntu/yaru

Ubuntu community theme "yaru". Better than a 🌯.

Language: SCSS - Size: 112 MB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

nanoporetech/hammerpede

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

Language: Python - Size: 946 KB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 3

nanoporetech/jmespath.js Fork of jmespath/jmespath.js

Javascript implementation of JMESPath, a query language for JSON

Size: 188 KB - Last synced at: 4 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

nanoporetech/onnxjs Fork of microsoft/onnxjs

ONNX.js: run ONNX models using JavaScript

Language: TypeScript - Size: 4.73 MB - Last synced at: 4 months ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 1

nanoporetech/fastq-filter

Quality and length filter for FastQ data

Language: Python - Size: 1.95 KB - Last synced at: 4 months ago - Pushed at: almost 8 years ago - Stars: 4 - Forks: 2

nanoporetech/linux4.9-minit

ONT fork of Linux for NVIDIA Tegra based devices

Language: C - Size: 985 MB - Last synced at: 4 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1

nanoporetech/marine-phage-paper-scripts

Language: Python - Size: 32.2 KB - Last synced at: 4 months ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 3

nanoporetech/barcoding

Naïve barcode deconvolution for amplicons

Language: Perl - Size: 427 KB - Last synced at: 4 months ago - Pushed at: about 8 years ago - Stars: 6 - Forks: 1

nanoporetech/getopt-win32

Language: C - Size: 16.6 KB - Last synced at: 18 days ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 4

nanoporetech/centrifuge Fork of DaehwanKimLab/centrifuge

Classifier for metagenomic sequences

Language: C++ - Size: 6.07 MB - Last synced at: 4 months ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

nanoporetech/u-boot

Language: C - Size: 134 MB - Last synced at: 4 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1

nanoporetech/mako

Analyte identification via squiggles.

Language: Python - Size: 7.02 MB - Last synced at: 4 months ago - Pushed at: about 7 years ago - Stars: 7 - Forks: 1