vdsearch: find viroids and viroid-like circRNAs

Finding viroids used to be a difficult task. Now it can be done in one line of code:

vdsearch easy-search my-transcriptome.fasta

Features

• End-to-end viroid-like RNA detection with one command
• Finds viroids (both families), satellite RNAs, ribozyviruses, and more
• De novo and reference-free
• Works for both transcriptomes and metatranscriptomes

Screenshots

Example usage

• Find viroid-like cccRNAs in a transcriptome or metatranscriptome

  vdsearch easy-search my-transcriptome.fasta

• Detect circularity from assembled contigs

  vdsearch find-circs my-transcriptome.fasta

• Cluster circRNAs

  vdsearch cluster --preset nt-cluster circRNAs.fasta

Installation

Using Docker

The easiest way to use vdsearch is to use the Docker image. This will install all dependencies for you and run the code in a virtual environment.

docker pull benjamindlee/vdsearch

Note: When using Docker, you will have to mount the directory containing your input files to the container. For example, if you have a file called my-transcriptome.fasta in the current directory, you can run the following command:

docker run -v $(pwd):/data benjamindlee/vdsearch easy-search /data/my-transcriptome.fasta

You may have to configure Docker to use more memory and CPUs. For example, if you have 16 CPUs and 64 GB of RAM, you can run the following command:

docker run -v $(pwd):/data --cpus 16 -m 64G benjamindlee/vdsearch easy-search /data/my-transcriptome.fasta

From source

If you want to run the code directly from source and will install dependencies (seqkit, etc.) yourself, please clone the repository and run the following commands:

git clone https://github.com/Benjamin-Lee/vdsearch.git
cd vdsearch

# activate a virtual environment (optional)
python3 -m venv venv
source venv/bin/activate

# install dependencies
pip install nimporter
pip install -e .

# test the installation
vdsearch --help

Contributing

Contributions are always welcome!

See contributing.md for ways to get started.

Support

For support, email [email protected] or join our Slack channel.

License

MIT

Citation

Lee, B. D., Neri, U., Roux, S., Wolf, Y. I., Camargo, A. P., Krupovic, M., RNA Virus Discovery Consortium, Simmonds, P., Kyrpides, N., Gophna, U., Dolja, V. V., & Koonin, E. V. (2023). Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs. Cell, 186(3), 646–661.e4. https://doi.org/10.1016/j.cell.2022.12.039