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

Analysis of sequencing error profile for long read data.

zeo++ fork of the LSMO

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

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

NanoASV official repo

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.

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.

Nanopore sequencing experimental protocols and computational pipelines

Species-level Taxonomic Abundance from 16S rRNA Sequencing (STARS)

LoRA, A Long Read Assembly pipeline for microbiome data

snakemake pipeline based on nanopolish

A bioinformatic pipeline for aligning amplicon reads to a DNA database based on Nextflow