Top 25 nanopore open source projects

Real-time species-typing visualisation for nanopore data.

✭ 13

javascript python HTML CSS shell nodejs bioinformatics nanopore bioinformatics-pipeline d3js minimap2 japsa

Predict plasmids from uncorrected long read data

✭ 27

python TeX Dockerfile bioinformatics research nanopore genomics pathogen bioinformatics-pipeline pacbio global-health kmer oxford-nanopore plasmid infectious-diseases long-reads uncorrected plasmidfinder

fast-sg

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

✭ 22

C++perl shell Makefile awk nanopore pacbio scaffolding illumina genome-assembly hybrid-genome-assembly alignment-free-algorithm

rkmh

Classify sequencing reads using MinHash.

✭ 42

C++HTML python bioinformatics nanopore openmp mutations minhash kmer

interARTIC

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

✭ 22

CSS HTML python shell javascript nanopore genomics covid19 artic-bioinformatics-platform

IsoQuant

Reference-based transcript discovery from long RNA read

✭ 26

python bioinformatics rna-seq nanopore ngs pacbio transcriptomics

Winnowmap

Long read / genome alignment software

✭ 151

c C++Makefile perl shell python nanopore pacbio genome-analysis

RATTLE

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

✭ 35

C++python bioinformatics rna-seq nanopore genomics clustering transcriptome

nanoflow

🔬 De novo assembly of nanopore reads using nextflow

✭ 20

Nextflow shell Makefile nanopore pipeline

vbz compression

VBZ compression plugin for nanopore signal data

✭ 31

C++CMake python c shell compression nanopore hdf5

nanoseq

Nanopore demultiplexing, QC and alignment pipeline

✭ 82

Nextflow groovy r python perl HTML workflow nanopore pipeline alignment qc demultiplexing nf-core

pychopper

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

✭ 74

python Makefile shell rna-seq nanopore transcriptomics cdna full-length

wub

Tools and software library developed by the ONT Applications group

✭ 57

python Makefile nanopore sequence-analysis nanopore-sequencing

pipeline-pinfish-analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish

✭ 27

python rna-seq nanopore genome-annotation transcriptomics cdna

taeper

A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.

✭ 18

python Makefile bioinformatics nanopore simulation

Clair3

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

✭ 119

python Jupyter Notebook c C++shell Dockerfile Makefile deep-learning nanopore genomics computational-biology variant-calling long-reads ont-data ont-models

poreCov

SARS-CoV-2 workflow for nanopore sequence data

✭ 34

Nextflow python shell r workflow bioinformatics nanopore basecalling artic sars-cov-2 nanopore-data

wengan

An accurate and ultra-fast hybrid genome assembler

✭ 81

perl nanopore pacbio hybrid illumina genome-assembler

haslr

A fast tool for hybrid genome assembly of long and short reads

✭ 68

C++python c Makefile bioinformatics nanopore genomics pacbio genome-assembly long-reads hybrid-assembly

pipeline-structural-variation

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

✭ 104

python nanopore whole-genome-sequencing structural-variation long-reads

pepper

PEPPER-Margin-DeepVariant

✭ 179

python C++c nanopore variants variant-calling oxford-nanopore genome-variation long-reads pacbio-ccs assembly-polishing

awesome-nanopore

A curated list of awesome nanopore analysis tools.

✭ 100

machine-learning bioinformatics nanopore awesome-list

poreplex

A versatile sequenced read processor for nanopore direct RNA sequencing

✭ 74

python c adapter rna-seq nanopore multiplexing barcoding

rerio

Research release basecalling models and configurations

✭ 60

python Roff nanopore basecalling

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

✭ 79

python javascript nanopore ngs metagenomics comparative-genomics kraken contamination clark robustness centrifuge low-biomass lmat

1-25 of 25 nanopore projects