Nextflow pipeline for analysis of direct RNA Nanopore reads

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).

Single cell Nanopore sequencing data for Genotype and Phenotype

A pipeline for high-quality bacterial genome construction using ONT sequencing

zeo++ fork of the LSMO

Analysis of sequencing error profile for long read data.

Pipeline to assemble oxford nanopore long sequencing reads and perform variant calling with long and short reads

NanoASV official repo

Supporting data for the publication "Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing"

Comprehensive pipeline for detection of TB from ONT adaptive sequencing and amplicon data.

Impact of lossy compression of nanopore raw signal data on basecall and consensus accuracy

HIV-64148, an integration of multiple long-read genome assemblers with a pipeline for analysis of HIV-1 genomic data from Oxford Nanopore Sequencing Technology or PacBio Real-Time (SMRT) Sequencing technology.

A generic best practice workflow for processing human Oxford Nanopore Technologies (ONT) sequencing data.

Nanopore sequencing experimental protocols and computational pipelines

Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline

PuntSeq - Chasing the microbial diversity of Cambridge's freshwater

This is just small command line pipeline to simplify going from ONT Unbasecalled data using Guppy to Assembly using Flye, all of the tools are existing tools.

An End-to-End GUI for real-time species identification via barcoded nanopore amplicon sequencing data. The pipeline is built using R Shiny library and majorly targets users with minimal coding background. Users can get from sequencing to results in a few clicks.

Snakemake pipeline for Base and functional QC for Fiberseq analysis using PacBio and Nanopore data. This pipeline was designed for the Lab of Sebastian Pott at UC