NEMO | Improved and accurate models for identification of 6mA using Nanopore sequencing

NEMO enables the study of N6-methyladenine at a single-base resolution in nanopore datasets. NEMO can be run in two different modes for methylation calling - one specific for GATC context (NEMO_R9_GATC), and one which is sequence context-agnostic (NEMO_R9_6mA).

Contents

Dependencies
Installation
Models
Usage
Generating Bed files

Dependencies

• Dorado Basecaller OR
• Bonito Basecaller
• modkit

Installation

NEMO can be downloaded by cloning from GitHub git clone [email protected]:SowpatiLab/NEMO.git

Available Models

Basecalling Models	Works with	Description
DORADO_MODELS/NEMO_R9_GATC	dorado	GaTC context model
BONITO_MODELS/NEMO_R9_GATC	bonito	GaTC context model
DORADO_MODELS/NEMO_R9_6mA	dorado	All context model
BONITO_MODELS/NEMO_R9_6mA	bonito	All context model

Usage

1. Basecalling

A. Using Dorado Models

---

6mA Calling in GATC context

dorado basecaller [email protected] POD5_DIR \
    --modified-bases-models DORADO_MODELS/NEMO_R9_GATC \
    --reference REFERENCE_GENOME > mod_calls.bam

6mA Methylation Calling

dorado basecaller [email protected] POD5_DIR \
    --modified-bases-models DORADO_MODELS/NEMO_R9_6mA \
    --reference REFERENCE_GENOME > mod_calls.bam

B. Using Bonito Models

---

6mA Calling in GATC context

bonito basecaller [email protected] POD5_DIR \
    --modified-base-model BONITO_MODELS/NEMO_R9_GATC.pt> \
    --reference REFERENCE_GENOME > mod_calls.bam

6mA Methylation Calling

bonito basecaller [email protected] POD5_DIR \
    --modified-base-model BONITO_MODELS/NEMO_R9_6mA.pt> \
    --reference REFERENCE_GENOME > mod_calls.bam

---

2. converting modBAM to bedMethyl using modkit

modkit pileup mod_calls.bam mod_calls.bed