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awesome-nanopore

A curated list of awesome nanopore analysis tools.

c3poa

Computational pipeline for calling consensi on R2C2 nanopore data

duplex-tools

Splitting of sequence reads by internal adapter sequence search

fastq-filter

Quality and length filter for FastQ data

hipore-c

We developed a protocol of in situ high throughput multi-way contact long read Pore-C sequencing (in situ HiPore-C), a strategy that integrated multi-fragment ligates preparation with third-generation sequencing technology. With HiPore-C approach, we could explore higher-order chromatin interaction genome-widely.

labjournal

Laboratory journal of Emil

m6anet

mandalorion-episode-ii

Version II of Mandalorion

master_of_pores

Nextflow pipeline for analysis of direct RNA Nanopore reads

megalodon

na12878

Data and analysis for NA12878 genome on nanopore

nanocount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2

notebooks

ont_tutorial_cdna_deseq2

bioinformatics tutorial demonstrating a simple workflow for cDNA based differential gene expression using minimap2, Rsubread and DESeq2

ont_tutorial_transcriptome

A bioinformatics tutorial demonstrating the application of long read cDNA sequence data for the identification of differentially expressed genes and transcripts

penguin

Penguin: A Tool for Predicting Pseudouridine Sites in Direct RNA Nanopore Sequencing Data

pipeline-polya-ng

Pipeline for calling poly(A) tail lengths from nanopore direct RNA data using nanopolish

pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

pore-c-snakemake

porechop

adapter trimmer for Oxford Nanopore reads

pychopper

A tool to identify full length cDNA reads

rageseq

RAGE-seq scripts

rampart

Read Assignment, Mapping, and Phylogenetic Analysis in Real Time

random

rnaseqdtu

RNA-seq workflow for differential transcript usage following Salmon quantification

spleeter

Deezer source separation library including pretrained models.

squigglekit

SquiggleKit: A toolkit for manipulating nanopore signal data

taiyaki

Training models for basecalling Oxford Nanopore reads

talon

Technology agnostic long read analysis pipeline for transcriptomes

talon-paper-2020

References and analyses for updated TALON paper