vdsearch's Introduction

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

Installation is still a work in progress since the code is still in beta. If you want to use it, 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

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