Finding viroids used to be a difficult task. Now it can be done in one line of code:
vdsearch easy-search my-transcriptome.fasta
- 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
-
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 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
Contributions are always welcome!
See contributing.md
for ways to get started.
For support, email [email protected] or join our Slack channel.
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), 646โ661.e4. https://doi.org/10.1016/j.cell.2022.12.039