OmniGenome is a comprehensive toolkit for genomic modeling and benchmarking. It provides a unified interface for various genomic modeling tasks, including genome sequence classification, regression and so on. OmniGenome is designed to be easy to use and flexible, allowing users to customize their workflows and experiment with different algorithms and parameters. It also includes a set of benchmarking tools to evaluate the performance of different genomic foundation models and compare their results.

• Click-to-run tutorials of Genomic sequence modeling
• Automated benchmarking of genomic foundation models
• Instant inference using pre-trained checkpoints
• Customizable pipeline for genomic modeling tasks

before installing OmniGenome, you need to install the following dependencies:

• Python 3.9+
• PyTorch 2.0+
• Transformers 4.37.0+

You can clone the repository and install it from source:

pip install -e .

This is the anonymized supplementary materials repository for the demonstration of the OmniGenome toolkit. This repository may not contain everything needed to run the toolkit, but it contains the main examples to demonstrate the toolkit's capabilities.

There is a click-to-run benchmarking example in OmniGenome, please refer to the benchmarking tutorial for more information.

There are several click-to-run tutorials in the tutorials directory that demonstrate how to use the toolkit for various genomic modeling tasks.

OmniGenome is licensed under the MIT License. See the LICENSE file for more information.