RepeatRanger: De Novo Repeat Annotation Tool for Assembled Genomes
Introduction
RepeatRanger is a powerful de novo repeat annotation tool designed for assembled genomes. It facilitates the identification and annotation of repetitive sequences within genome assemblies without relying on prior knowledge or reference data.
Repetitive elements, such as transposons, satellites, and simple sequence repeats, can comprise a significant portion of many genomes. Accurate identification and characterization of these repeats are crucial for understanding genome structure, evolution, and function. RepeatRanger employs advanced algorithms to efficiently detect and annotate repetitive regions, providing valuable insights for downstream analyses.
Note: RepeatRanger is currently under active development and not yet ready for production use. We encourage users to explore the tool and provide feedback to help shape its future development.
Features
- Kmer-based search: The tool supports searching for repeat instances based on seed sequences or k-mers, allowing for flexible and customizable repeat detection.
Installation
RepeatRanger can be easily installed via pip:
pip install repeatranger
Usage
Currently, RepeatRanger can be used to search for all repeat instances in a genome assembly based on a provided seed sequence or k-mer. The command-line usage is as follows:
repeatranger -f <your_genome.fa> -o <output_file.fa> -i <kmer>
-for--fasta: Specify the path to your genome assembly in FASTA format.-oor--output: Specify the path and filename for the output file containing the identified repeat instances.-ior--kmer: Provide the k-mer sequence or seed to use for repeat instance detection.
For more detailed usage instructions and advanced options, please refer to the tool's documentation or run repeatranger --help.
Contributing
We welcome contributions to RepeatRanger from the community. If you encounter any issues, have feature requests, or would like to contribute code improvements, please open an issue or submit a pull request on the GitHub repository.
License
RepeatRanger is released under the MIT License.
Contact
For any questions, suggestions, or inquiries, please contact the project maintainers at ad3002@gmail.com.
1 maintainer
Metadata
1 maintainer
Release files for RepeatRanger 0.1.2
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