densecall 0.0.2

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DenseCall2

DenseCall2: De Novo Base-Calling of DNA Modifications Using Nanopore Sequencing

Contents

• DenseCall2
  • Contents
  • Requirements
    • Hardware
    • Software
  • Installation
    • DenseCall2
    • Basecalling of FAST5/Pod5 Files
  • Usage Notes
    • Training Your Own Basecalling Model (Optional)
  • Knowledge distilation
  • Downstream Analysis
  • Citing
  • License
  • Acknowledgement

DenseCall2 is an updated base-caller built on an optimized Conformer architecture for nanopore signal processing, enabling simultaneous base-calling and modification detection.

Requirements

Hardware

• RAM: 2 GB minimum; 16 GB or more recommended
• CPU: 4 cores minimum, ≥ 2.3 GHz per core
• GPU: NVIDIA RTX 4090 or newer (required for DenseCall2)

Benchmarks were collected on an ASUSTeK SVR TS700-E9-RS8 workstation
(Xeon Silver 4214 @ 2.20 GHz, 64 GB RAM, RTX 4090 24 GB).

Software

Supported Operating Systems

• Linux: Ubuntu 22.04 or newer
• Windows and macOS are not yet supported

Python

• Version 3.10 or higher is required
  Install on Ubuntu with:

  sudo apt update
  sudo apt install python3 python3-pip
  

Installation

DenseCall2

First, set up a new environment and install the necessary Python packages using conda and pip:

# Create a new conda environment
conda create -n densecall python=3.10 -y
conda activate densecall

# Upgrade pip
pip install --upgrade pip

# Download and install 
git clone https://github.com/LuChenLab/DENSECALL2.git
cd DENSECALL2
pip install -r requirements.txt
pip install flash-attn==2.8.3 --no-build-isolation --no-cache-dir
python setup.py develop

DenseCall2 is compatible with the basecaller of ont-bonito, allowing our trained models to be used for the basecalling process. Install ont-bonito as follows:

cd ont-bonito-0.7.3
python setup.py develop

Basecalling of FAST5/Pod5 Files

After installing DenseCall2, download the pre-trained models for human-specific models from Pre-trained Basecalling Models. Available models include [e-mail] for r9.4.1 data and [e-mail] for r10.4.1 data.

DenseCall2 provides a method for transforming .fast5 files into .fastq format or .sam format. Follow the commands below to perform basecalling:

# Activate the DenseCall2 conda environment
conda activate densecall2

# Navigate to the directory where you want to download the models
cd /path/to/Densecall2/densecall/models/

# Download and extract the models
# Note: Ensure you have already downloaded the .tar.gz files to this directory
tar -xzvf [e-mail] 

# Perform basecalling on the .fast5 files to generate .fastq files 
densecall basecaller dna_r9.4.1_hac_m5C@v1.0 /path/to/fast5_data/ --mod --chunksize 12000 --overlap 600 --reference chr22.mmi --recursive --alignment-threads 12 > mod.sam

If you are using the tool solely for standard basecalling, you can omit the --mod flag.

densecall basecaller dna_r9.4.1_hac_m5C@v1.0 /path/to/fast5_data/ --chunksize 12000 --overlap 600  > mod.fastq

Usage Notes

• Modified-base calling
  Add --mod together with --reference and ensure the output file has a .sam extension.
  DenseCall2 will perform Viterbi decoding and append MM/ML tags to the SAM output.

• Standard base calling
  Omit --mod and set the output extension to .fastq or .fq.
  DenseCall2 will use beam-search decoding.

Training Your Own Basecalling Model (Optional)

densecall train - train a DenseCall2 model

To train a model using your own reads, first get a trained model from Remora.

remora model download 

densecall basecaller dna_r10.4.1_e8.2_400bps_hac@v3.5.2 ./chr1_fast5 --batchsize 64 --chunksize 5000  --overlap 100 \
--reference chr1.mmi --recursive --save-ctc --min-accuracy-save-ctc 0.9 \
--alphabet NACZGT \
--modified-codes Z \
--modified-base-model /path/to/dna_r10.4.1_e8.2_400bps_hac_v3.5.1_5mc_CG_v2.pt \
--max-reads 100000 > r10_train_data/test.sam

Training a new model from scratch:

densecall train test --directory r10_train_data/ -f --batch 64 --epochs 30 \
--no-quantile-grad-clip --lr 0.002 --alphabet NACZGT \
--config conformer.toml --new --compile

Knowledge distilation

To train a model using knowledge distilation, add the --teacher flag to the training command.

densecall train r10_student  --directory r10_train_data/ -f --batch 64  --epochs 20  --grad-accum-split 2 --no-quantile-grad-clip --lr 0.002    --alphabet NACZGT --config conformer_fast.toml   --new --compile --teacher r10_teacher/

All training calls use Automatic Mixed Precision to speed up training.

Downstream Analysis

The results were analyzed using the ONT tool modkit, which processes BAM files containing MM/ML tags to generate comprehensive statistical reports. This study specifically employed modkit's "validate" and "pileup" functions.

Citing

A pre-print will be uploaded soon.

License

GNU General Public License v3.0

Acknowledgement

We thank Bonito for making its source code available. DenseCall2 was built on Bonito’s framework: the save-CTC module, the training pipeline and the conversion of Conformer-based basecall outputs to base sequences have all been modified from Bonito’s original implementation. Bonito’s licence can be found here.