The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

simON-reads ("Simulate Oxford Nanopore Reads") is a simple yet powerful tool to generate fastq files containing MiniON-like long reads

Nanopore sequence read simulator

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Tools for plotting methylation data in various ways

Structural variant caller for real-time long-read sequencing data

GUI/CommandLine Tool Box for biologistists to utilize NGS data.

Oxford Nanopore's Basecaller

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

Haplotype aware de novo assembly of diploid genome from long reads

Read-based phasing of genomic variants, also called haplotype assembly

Generate an interactive dot plot from mummer or minimap alignments

Dotplot large Genomes in an Interactive, Efficient and Simple way

Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

Genome assembly evaluation tool

De novo assembly from Oxford Nanopore reads.

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

Toolset for SV simulation, comparison and filtering

Long read based human genomic structural variation detection with cuteSV

Structural variation caller using third generation sequencing

An overview of all nanopack tools

Plotting scripts for long read sequencing data

Copy number variant detection from targeted DNA sequencing

a Shiny/R application to view and annotate copy number variations

Tool for finding matches to degenerate sequence motifs in FASTA files.

A genome-scale, fast, and precise segmental duplications mapping tool

Uniform Manifold Approximation and Projection