TeloTracker

Yeast Telomere Identification in Nanopore Reads

TeloTracker is a Python package designed to track and visualize Oxford Nanopore Technology (ONT) Sequencing of yeast telomeres. It was specifically developed to study Alternative Lengthening of Telomeres (ALT) in yeast, but it can be used for general telomere analysis in Saccharomyces cerevisiae.

🔧 Installation

To install TeloTracker, you can clone this repository by running the command below.

git clone https://github.com/Jacob-M-Wells/TeloTracker.git
cd TeloTracker

Installing with conda (recommended)

conda env create -n telotracker -f environment.yml
conda activate telotracker

Installing with pip

pip install -r requirements.txt

Note: Several required tools are not available on PyPI and must be installed separately if using pip. Using conda is highly recommended to avoid missing dependencies.

To avoid missing dependencies, installing with Conda is strongly recommended (see above).

The following external tools are required:

• BLAST+ (version 2.16.0)
• RepeatMasker (version 4.1.7-p1)
• Porechop_ABI (≥0.5.0)
• Clustal Omega (version 1.2.4)
• Flye (version 2.9.5)
• Minimap2 (version 2.28)
• QUAST (version 5.3.0)
• Medaka (version 2.0.1)
• MUMmer (version 3.23)
• MUSCLE (version 5.3)
• SAMtools & BCFtools (version 1.21)
• BEDtools (version 2.31.1)
• RMBlast (version 2.14.1)

Installing Dorado (Required for Basecalling)

Dorado is a high-performance, open source basecaller for Oxford Nanopore reads. Dorado can be run with a docker container or installed locally.

Dorado must be used to basecall (rather than using MinKnow), as basecalling without trimming adapters/barcode sequences is required.

📝 Detailed instructions and usage examples are available in the Dorado documentation.

Option 1. Run with Docker Container (using singularity)

📦 Download the latest release for your platform from the Dorado Docker Releases page.

singularity pull dorado.sif docker://nanoporetech/dorado:latest
singularity exec dorado.sif dorado --help

Option 2. Run with local installation

📦 Download the latest release for your platform from the Dorado GitHub Releases page. The current version as of 03/13/2025: Dorado 0.9.1 @ https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.9.1-linux-x64.tar.gz

wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.9.1-linux-x64.tar.gz
gunzip https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.9.1-linux-x64.tar.gz
tar -xvf https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.9.1-linux-x64.tar.gz
mv dorado-0.9.1-linux-x64/ ~/bin/
ln -s ~/bin/dorado-0.9.1-linux-x64/bin/dorado ~/bin/dorado
source ~/.bashrc
dorado --help

Usage

TeloTracker processes ONT waveform data (.pod5/.fast5 files) to basecall and analyze reads for their telomere and sub-telomere features. TeloTracker has two distinct pipelines: reference and track.

• reference: creates a telomere reference genome and annotation
• track: analyzes reads against a reference for telomere dynamics

Quick Start

1. Generate a reference

   telotracker reference
   -r input_reads.fastq
   -o teloref_outdir
   -t 16

2. Track telomeres in new reads

   telotracker track
   -i new_reads.fastq
   -ref teloref_outdir/reference.fasta
   -o tracking_outdir
   -t 16

3. Optional: Basecall and demultiplex from .pod5

   telotracker basecall
   -p raw_input.pod5
   -o basecall_outdir
   -m sup
   -t 8

Citing

If you use TeloTracker in your research, please cite this GitHub repository:

Wells, Jacob M. TeloTracker. https://github.com/Jacob-M-Wells/TeloTracker