awesome-nanopore

List of software packages for Nanopore sequencing data analysis, including basecalling, DNA/RNA modifications, etc. Contributions welcome...

Software packages

Basecalling

• Nanocall - [C++] - Nanocall: an open source basecaller for Oxford Nanopore sequencing data
• PoreSeq - [C++] - De novo sequencing and variant calling with nanopores using PoreSeq
• Nanonet - [C++] - Nanonet - Development version of RNN basecaller
• DeepNano - [Python] - DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads
• BasecRAWller - [Close sourced (May request code by emailing [email protected])] - BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal
• Chiron - [Python] - Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning
• Causalcall - [Python] - Causalcall: Nanopore Basecalling Using a Temporal Convolutional Network
• Bonito - [Python] - A PyTorch Basecaller for Oxford Nanopore Reads

ReadUntil Real-time mapping

• Readfish - [Python] - Readfish enables targeted nanopore sequencing of gigabase-sized genomes
• UNCALLED - [C++] - Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
• SquiggleNet - [Python] - Real-Time, Direct Classification of Nanopore Signals with SquiggleNet

Segmentation

• tombo resquiggle - [Python] - Re-squiggle Algorithm.
• nanopolish eventalign - [C++] - Detecting DNA cytosine methylation using nanopore sequencing.

DNA modification analysis

• nanopolish call-methylation - [C++] - Detecting DNA cytosine methylation using nanopore sequencing.
• nanoNOMe - [Python] - Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
• signalAlign - [C] - Mapping DNA methylation with high-throughput nanopore sequencing.
• mCaller - [Python] - Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.
• DeepSignals - [Python] - DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning.
• tombo detect_modifications - [Python] - (previously nanoraw)De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing.
• NanoMod - [Python] - NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data.

RNA modification analysis

• tombo detect_modifications - [Python] - Modified Base Detection.
• MINES - [Python] - Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base specific resolution.
• EpiNano - [Python] - Accurate detection of m6A RNA modifications in native RNA sequences.
• Nanom6A - [Python] - Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing.
• m6anet - [Python] - Detection of m6A from direct RNA-Seq data.
• nano-ID - [R] - Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms.
• nanoRMS - [Python] - Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing.
• Yanocomp - [Python] - Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads.
• DiffErr - [Python] - A tool for detecting modifications from Nanopore DRS errors using a low modification control.
• ELIGOS - [Python] - Decoding the epitranscriptional landscape from native RNA sequences.
• nanoDoc - [Python] - nanoDoc: RNA modification detection using Nanopore raw reads with Deep One-Class Classification.
• nanocompore - [Python] - RNA modifications detection by comparative Nanopore direct RNA sequencing.
• DRUMMER - [Python] - Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing.
• xPore - [Python] - Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore.

RNA structure prediction

• nanoSHAPE - [Python] - Direct detection of RNA modifications and structure using single molecule nanopore sequencing.
• PORE-cupine - [R] - Determination of isoform-specific RNA structure with nanopore long reads.

Poly(A) tail length estimation

• nanopolish polya - [C++] - Nanopore native RNA sequencing of a human poly(A) transcriptome.
• tailfindr - [R] - tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing.

Transcript discovery and quantification

• bambu - [R] - Reference-guided isoform reconstruction and quantification for long read RNA-Seq data
• NanoSplicer - [Python] - Identification of splice junctions from nanopore sequencing using raw signal squiggles

Contributing

We welcome contributions and suggestions! Please follow the steps below to contribute:

1. Fork this repository
2. Make a change to README.md in this format: [RESOURCE](LINK) - [language(s)] - DESCRIPTION
3. Submit a pull request.

Citation

Wan, Y.K., Hendra, C., Pratanwanich, P.N. & Göke, J. Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. Trends in Genetics (2021). https://doi.org/10.1016/j.tig.2021.09.001.

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According to the official awesome Github repository, an awesome list on GitHub is "a curation of actual awesome stuff", so an awesome list only includes items that has been reseached on by a contributor who would personally recommend the items. To learn more, please read the official awesome manifesto.

Contact

This repository was created by Yuk Kei Wan.