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awesome-nanopore

A curated list of awesome nanopore analysis tools.
https://github.com/GoekeLab/awesome-nanopore

Last synced: about 9 hours ago
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  • Software packages

    • Basecalling

      • Close sourced (May request code by emailing [email protected])
      • Dorado - [C++] - Production basecaller from 2022, successor to Guppy.
      • Nanocall - [C++] - [Nanocall: an open source basecaller for Oxford Nanopore sequencing data](https://academic.oup.com/bioinformatics/article/33/1/49/2525680)
      • PoreSeq - [C++] - [De novo sequencing and variant calling with nanopores using PoreSeq](https://www.nature.com/articles/nbt.3360)
      • Nanonet - [C++] - [Nanonet - Development version of RNN basecaller](https://github.com/ProgramFiles/nanonet)
      • DeepNano - [Python] - [DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178751)
      • Chiron - [Python] - [Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning](https://academic.oup.com/gigascience/article/7/5/giy037/4966989)
      • Causalcall - [Python] - [Causalcall: Nanopore Basecalling Using a Temporal Convolutional Network](https://www.frontiersin.org/articles/10.3389/fgene.2019.01332/full)
      • Bonito - [Python] - A PyTorch Basecaller for Oxford Nanopore Reads (research, not production basecaller)

    • Segmentation

      • tombo resquiggle - [Python] - [Re-squiggle Algorithm](https://nanoporetech.github.io/tombo/resquiggle.html).

    • Raw signal data manipulation, conversion, visualisation, etc.

      • pyslow5 - [Python] - [pyslow5 python library
      • slow5lib - [C] - [Fast nanopore sequencing data analysis with SLOW5
      • slow5tools - [C/C++] - [Toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format](https://hasindu2008.github.io/slow5tools/)
      • SquiggleKit SquigglePlot - [Python] - [SquiggleKit: a toolkit for manipulating nanopore signal data](https://academic.oup.com/bioinformatics/article/35/24/5372/5537108)

    • Adaptive sampling / ReadUntil Real-time mapping / signal mapping

      • Readfish - [Python] - [Readfish enables targeted nanopore sequencing of gigabase-sized genomes](https://www.nature.com/articles/s41587-020-00746-x)
      • UNCALLED - [C++] - [Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED](https://www.nature.com/articles/s41587-020-0731-9)
      • SquiggleNet - [Python] - [Real-Time, Direct Classification of Nanopore Signals with SquiggleNet](https://www.biorxiv.org/content/10.1101/2021.01.15.426907v2)
      • Sigmap - [C/C++] - [Real-time mapping of nanopore raw signals
      • cwDTW - [C/C++] - [An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing](https://academic.oup.com/bioinformatics/article/34/17/i722/5093233)
      • OpenDBA - [C++/CUDA] - [GPU-accelerated Dynamic Time Warp (DTW) Barycenter Averaging](https://github.com/nodrogluap/OpenDBA#how-do-i-use-this-for-oxford-nanopore-data)
      • Magenta & Maxwell - [C++/CUDA] - [Fast signal-level matching for direct RNA nanopore sequencing](https://github.com/nodrogluap/maxwell)

    • RNA modification analysis

      • DiffErr - [Python] - A tool for detecting modifications from Nanopore DRS errors using a low modification control.
      • MINES - [Python] - [Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base specific resolution](https://rnajournal.cshlp.org/content/early/2019/10/17/rna.072785.119).
      • EpiNano - [Python] - [Accurate detection of m6A RNA modifications in native RNA sequences](https://www.nature.com/articles/s41467-019-11713-9).
      • Nanom6A - [Python] - [Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02241-7).
      • m6anet - [Python] - [Detection of m6A from direct RNA sequencing using a multiple instance learning framework](https://www.nature.com/articles/s41592-022-01666-1).
      • nano-ID - [R] - [Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms](https://genome.cshlp.org/content/30/9/1332.full).
      • nanoRMS - [Python] - [Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing](https://www.nature.com/articles/s41587-021-00915-6?proof=t%3B).
      • Yanocomp - [Python] - [Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads](https://www.biorxiv.org/content/10.1101/2021.06.15.448494v1).
      • ELIGOS - [Python] - [Decoding the epitranscriptional landscape from native RNA sequences](https://academic.oup.com/nar/article/49/2/e7/5876284).
      • nanoDoc - [Python] - [nanoDoc: RNA modification detection using Nanopore raw reads with Deep One-Class Classification](https://www.biorxiv.org/content/10.1101/2020.09.13.295089v1).
      • nanocompore - [Python] - [RNA modifications detection by comparative Nanopore direct RNA sequencing](https://www.biorxiv.org/content/10.1101/843136v1).
      • DRUMMER - [Python] - [Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing](https://www.nature.com/articles/s41467-020-19787-6.pdf?origin=ppub).
      • xPore - [Python] - [Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore](https://doi.org/10.1038/s41587-021-00949-w).
      • tombo detect_modifications - [Python] - [Modified Base Detection](https://nanoporetech.github.io/tombo/modified_base_detection.html).
      • Magnipore - [Python] - [Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples](https://doi.org/10.1101/2023.03.17.533105)
      • DENA - [Python/R] - [DENA: training an authentic neural network model using Nanopore sequencing data of Arabidopsis transcripts for detection and quantification of N6-methyladenosine on RNA](https://doi.org/10.1186/s13059-021-02598-3)
      • mAFiA - [Python] - [Detecting m6A at single-molecular resolution via direct RNA sequencing and realistic training data](https://doi.org/10.1038/s41467-024-47661-2)
      • Penguin - [Python] - [Penguin: A Tool for Predicting Pseudouridine Sites in Direct RNA Nanopore Sequencing Data](https://doi.org/10.1016/j.ymeth.2022.02.005)

    • DNA modification analysis

      • modkit - [Rust] - Extract modified base calls from dorado BAM output to bedMethyl format, also calculate DMRs
      • Megalodon - [C++] - Research modified base caller which uses rerio, remora and a genome (deprecated by ONT 2023 for Dorado).
      • modbam2bed - [C++] - Convert modified base calls from megalodon etc to bedMethyl format (deprecated by ONT 2023 for Modkit)
      • nanoNOMe - [Python] - [Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing](https://www.nature.com/articles/s41592-020-01000-7).
      • signalAlign - [C] - [Mapping DNA methylation with high-throughput nanopore sequencing](https://www.nature.com/articles/nmeth.4189).
      • mCaller - [Python] - [Single-molecule sequencing detection of N6-methyladenine in microbial reference materials](https://www.nature.com/articles/s41467-019-08289-9).
      • DeepSignals - [Python] - [DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning](https://academic.oup.com/bioinformatics/article/35/22/4586/5474907).
      • NanoMod - [Python] - [NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5372-8).
      • f5c call-methylation - [C/C++/CUDA] - [GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03697-x)

    • RNA structure prediction

      • nanoSHAPE - [Python] - [Direct detection of RNA modifications and structure using single molecule nanopore sequencing](https://www.biiorxiv.org/content/10.1101/2020.05.31.126763v1).
      • PORE-cupine - [R] - [Determination of isoform-specific RNA structure with nanopore long reads](https://www.nature.com/articles/s41587-020-0712-z).

    • Poly(A) tail length estimation

      • tailfindr - [R] - [tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing](https://rnajournal.cshlp.org/content/early/2019/07/02/rna.071332.119).
      • nanopolish polya - [C++] - [Nanopore native RNA sequencing of a human poly(A) transcriptome](https://www.nature.com/articles/s41592-019-0617-2?proof=t).

    • Transcript discovery and quantification

      • RNAbloom2 - [Java] - [Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2](https://www.nature.com/articles/s41467-023-38553-y)
      • RATTLE - [C++] - [RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02715-w)
      • bambu - [R] - [Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu](https://rdcu.be/deluQ)
      • NanoSplicer - [Python] - [Identification of splice junctions from nanopore sequencing using raw signal squiggles](https://academic.oup.com/bioinformatics/article/38/15/3741/6594111)
      • TALON - [Python] - [Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets](https://www.biorxiv.org/content/10.1101/672931v2) **Run before** [TranscriptClean](https://github.com/mortazavilab/TranscriptClean)
      • trackcluster - [Python] - [trackcluster is an isoform calling and quantification pipeline for long RNA/cDNA reads](https://genome.cshlp.org/content/30/2/287.short)
      • FLAIR - [Python] - [Full-Length Alternative Isoform analysis of RNA](https://www.nature.com/articles/s41467-020-15171-6)

    • Genome Assembly

      • Flye - [C++] - Single molecule sequence assembler with good polishing capabilities
      • Shasta - [C] - Very fast and capable nanopore assembler

    • Single-cell analysis

      • BLAZE - [Python] - [Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE](https://www.biorxiv.org/content/10.1101/2022.08.16.504056v1)

  • Contact

  • Pipelines

    • Single-cell analysis

      • MOP2 - [Nextflow] - [MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets](https://www.frontiersin.org/articles/10.3389/fgene.2020.00211/full)
      • nf-core/nanoseq - [Nextflow] - [A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines](https://www.biorxiv.org/content/10.1101/2021.04.21.440736v1)

    • Metagenomics

      • nf-Wochenende - [Nextflow, Python] - [Wochenende - modular and flexible alignment-based shotgun metagenome analysis](https://www.biorxiv.org/content/10.1101/2022.03.18.484377v3)

    • Reads simulation

      • NanoSim - [Python] - [NanoSim: nanopore sequence read simulator based on statistical characterization.](https://doi.org/10.1093/gigascience/gix010), [Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data.](https://academic.oup.com/gigascience/article/9/6/giaa061/5855462?login=true), [Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim.](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad013/7080817?login=true)

  • What is an awesome list?

Programming Languages
Python 27 C++ 11 C 5 R 4 Jupyter Notebook 3 Nextflow 2 Red 1 Java 1 Rust 1
Categories
Software packages 62 Pipelines 4 What is an awesome list? 1 Contact 1
Sub Categories
RNA modification analysis 18 Basecalling 9 DNA modification analysis 9 Adaptive sampling / ReadUntil Real-time mapping / signal mapping 7 Transcript discovery and quantification 7 Raw signal data manipulation, conversion, visualisation, etc. 4 Reads simulation 3 Single-cell analysis 3 Genome Assembly 2 RNA structure prediction 2 Poly(A) tail length estimation 2 Segmentation 1 Metagenomics 1
Keywords
nanopore 14 bioinformatics 8 rna-seq 6 nanopore-sequencing 5 genomics 4 oxford-nanopore 4 rna 3 methylation 3 transcriptome 3 cdna 2 transcriptomics 2 pacbio 2 r 2 transcript-quantification 2 nextflow 2 pipeline 2 rna-modifications 2 basecalling 2 epigenetics 2 sequencing 2 ont 2 single-cell-rna-seq 1 pacbio-sequencing 1 denovo-assembly 1 bulk-rna-seq 1 bioinformatics-tool 1 libtorch 1 pytorch 1 adaptive-sampling 1 modified-bases 1 python 1 modification 1 tensorflow 1 predict-rna-modifications 1 machine-learning 1 rna-modification-stoichiometry 1 tombo-resquiggling 1 raw-signal 1 epitranscriptomics 1 epigenomics 1 comparative-analysis 1 science 1 genome-assembly 1 c-plus-plus 1 unicorns 1 resources 1 lists 1 awesome-list 1 awesome 1 simulator 1