Science Score: 57.0%
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✓codemeta.json file
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✓DOI references
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○Scientific vocabulary similarity
Low similarity (13.5%) to scientific vocabulary
Repository
Viroid-like circRNA discovery and analysis suite
Basic Info
Statistics
- Stars: 15
- Watchers: 3
- Forks: 2
- Open Issues: 11
- Releases: 0
Metadata Files
README.md
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:
sh
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
sh
vdsearch easy-search my-transcriptome.fasta
- Detect circularity from assembled contigs
sh
vdsearch find-circs my-transcriptome.fasta
- Cluster circRNAs
sh 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.
bash
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:
bash
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:
bash
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:
```bash 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 benjamin.lee@chch.ox.ac.uk or join our Slack channel.
License
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
Owner
- Name: Benjamin Lee
- Login: Benjamin-Lee
- Kind: user
- Location: Tysons, VA
- Website: benjamindlee.com/about
- Repositories: 10
- Profile: https://github.com/Benjamin-Lee
NIH-OxCam scholar at @ncbi & DPhil student at Oxford. Previously @Harvard CS '20 and @IQTLabs
Citation (CITATION.cff)
cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: Viroid-like circRNA discovery and analysis suite
authors:
- family-names: Lee
given-names: Benjamin D.
- family-names: Neri
given-names: Uri
- family-names: Roux
given-names: Simon
- family-names: Wolf
given-names: Yuri I.
- family-names: Camargo
given-names: Antonio Pedro
- family-names: Krupovic
given-names: Mart
- family-names: Simmonds
given-names: Peter
- family-names: Kyrpides
given-names: Nikos
- family-names: Gophna
given-names: Uri
- family-names: Dolja
given-names: Valerian V.
- family-names: Koonin
given-names: Eugene V.
preferred-citation:
type: article
title: Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs
authors:
- family-names: Lee
given-names: Benjamin D.
- family-names: Neri
given-names: Uri
- family-names: Roux
given-names: Simon
- family-names: Wolf
given-names: Yuri I.
- family-names: Camargo
given-names: Antonio Pedro
- family-names: Krupovic
given-names: Mart
- family-names: Simmonds
given-names: Peter
- family-names: Kyrpides
given-names: Nikos
- family-names: Gophna
given-names: Uri
- family-names: Dolja
given-names: Valerian V.
- family-names: Koonin
given-names: Eugene V.
journal: Cell
volume: '186'
issue: '3'
year: '2023'
issn: 0092-8674
doi: 10.1016/j.cell.2022.12.039
url: https://www.sciencedirect.com/science/article/pii/S0092867422015823
abstract: Summary Viroids and viroid-like covalently closed circular (ccc) RNAs
are minimal replicators that typically encode no proteins and hijack cellular
enzymes for replication. The extent and diversity of viroid-like agents are poorly
understood. We developed a computational pipeline to identify viroid-like cccRNAs
and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The
search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters,
a 5-fold increase compared to the previously identified viroid-like elements.
Within this diverse collection, we discovered numerous putative viroids, satellite
RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual
ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified
in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like
cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and
ecosystems implies that their host range is far broader than currently known,
and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.
start: 646-661.e4
GitHub Events
Total
- Issues event: 1
- Watch event: 1
- Issue comment event: 2
- Fork event: 1
Last Year
- Issues event: 1
- Watch event: 1
- Issue comment event: 2
- Fork event: 1
Dependencies
- nimlang/nim 1.6.10 build
- click-didyoumean *
- igraph *
- matplotlib *
- pandas *
- pycirclize *
- rich *
- rich_click *
- scikit-bio *
- shellingham *
- typer <0.6