Nanopore sequence read simulator

Assembly and binning of metagenomes

Reference-guided transcript discovery and quantification for long read RNA-Seq data

Identification of differential RNA modifications from nanopore direct RNA sequencing

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

Detecting methylation using signal-level features from Nanopore sequencing reads

Training models for basecalling Oxford Nanopore reads

🌺 reference-free transcriptome assembly for short and long reads

Nextflow pipeline for analysis of direct RNA Nanopore reads

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

Simple bacterial assembly and annotation pipeline

Tools and software library developed by the ONT Applications group

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).

DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads

Nanopore data analysis in R

The first app for Mobile DNA Sequence Alignment and Analysis

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.

NANOME pipeline (Nanopore long-read sequencing consensus DNA methylation detection method and pipeline)