NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
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Updated
May 24, 2024 - Python
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
Simple bacterial assembly and annotation pipeline
RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)
"nanoCEM" is a simple tool designed to visualize the features that distinguish between two groups of ONT data at the site level.
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
a deep neural network model for mapping modifications in nanopore Long-read sequencing data
Assembly and binning of metagenomes
Mask Pathogens for Outbreak Analysis
MinION Classification & Alerting System
VIral GEnome ASsembly pipelines for WGS
A tool to filter short artificial deletion variations by Oxford Nanopore Technologies R9 and R10 flow cells and chemistries.
Marcus Viscardi's personal scripts used to analyze outputs of dRNA seq w/ ONT. Please feel free to reach out if you are interested in utilizing any of this code!
Identification of differential RNA modifications from nanopore direct RNA sequencing
Giraffe_View is designed to help assess and visualize the accuracy of long-read sequencing datasets.
DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
Consensus calling for tiling amplicon nanopore sequencing
This repository is the current repository for our Jones et al. 2024 manuscript titled Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage.
This is the repository for the manuscript “Expanding the transcriptomic toolbox in prokaryotes by Nanopore sequencing of RNA and cDNA molecules.” In this study, we applied and benchmarked all currently available RNA-seq kits from Oxford Nanopore technologies to analyse RNAs in the prokaryotic model organism Escherichia coli K-12.
NanoML-5moU: A Machine Learning framework to detect 5mou modification in IVT direct RNA sequencing data
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