From: Opportunities and challenges in long-read sequencing data analysis

Tool | Base modifications | Strategy | Reference |
---|---|---|---|

Guppy | 5mCpG, 5mC (Dcm), 6mA (Dam) | Basecall | [45] |

Taiyaki | – | Basecall | [45] |

RepNano | BrdU | Basecall | [109] |

D-Nascent | BrdU | HMM | [95] |

Nanopolish | 5mCpG | HMM | [66] |

Megalodon | 6mA, 5mCpG | HMM | [45] |

signalAlign | 6mA, 5mC, 5hmC | HMM-HDP | [107] |

DeepSignal | 6mA (Dam), 5mCpG | Neural network (CNN + classifier) | [110] |

DeepMod | 6mA, 5mCpG | Neural network (LSTM-RNN) | [111] |

mCaller | 6mA, 5mCpG | Neural network classifier | [108] |

Tombo | 6mA (DNA), 5mC (RNA, DNA), de novo | Statistical test | [105] |

NanoMod | de novo | Statistical test | [106] |

EpiNano | m6A (RNA) | SVM | [112] |