CulebrONT: Simplifying Genome Assembly with Oxford Nanopore Technologies
With the advent of long-read sequencing technologies like Oxford Nanopore Technologies (ONT), genome assembly has become more efficient and accurate. However, the abundance of assembly tools available can make it challenging for researchers to determine the most suitable one for their specific organisms. This is where CulebrONT comes in.
CulebrONT is an open-source, scalable, and traceable snakemake pipeline designed to simplify the genome assembly process using long-read data from ONT sequencing. Its primary goal is to increase contiguity and accuracy by effectively solving repeats and structural variants in both prokaryotic and eukaryotic genomes.
One of the key features of CulebrONT is its ability to launch multiple assembly tools in parallel. By leveraging parallel computing, researchers can significantly reduce the time it takes to find the best assembly method for their organisms. This feature is crucial for handling the ever-increasing number of assembly tools released or updated weekly.
To start using CulebrONT, researchers are advised to perform base-calling and quality control on their ONT sequencing data. This can be done using the baseDmux tool, which allows for the multiplexing of libraries across several Minion runs. The output files can then be gathered by genome for subsequent steps in the CulebrONT pipeline.
CulebrONT’s modular design ensures scalability and adaptability for different research scenarios. Its traceability feature enables researchers to track the entire assembly process, making it easier to reproduce results and troubleshoot any issues that arise.
In terms of technology, CulebrONT is built on Snakemake, a powerful workflow management system that simplifies the creation and execution of complex pipelines. It also requires Singularity, a containerization tool that allows for reproducibility and portability of the pipeline across different computing environments.
To ensure comprehensive documentation and support, CulebrONT provides a detailed user guide hosted on Read the Docs. This guide offers step-by-step instructions on how to install, configure, and run the pipeline. Additionally, the CulebrONT community actively maintains the pipeline, providing updates and addressing any reported issues.
In conclusion, CulebrONT is a valuable tool for researchers seeking to streamline and improve genome assembly using ONT long-read data. Its scalability, modularity, and traceability features make it an indispensable asset in the genomics research community. By leveraging parallel computing and offering a wide range of assembly tools, CulebrONT significantly enhances the contiguity and accuracy of genome assemblies. Researchers can access the pipeline through its documentation on Read the Docs and benefit from the community’s continuous maintenance and support.
If you have any questions about CulebrONT or its implementation in your research, please feel free to ask.
References:
- CulebrONT GitHub Repository: https://github.com/SouthGreenPlatform/culebrONT
- CulebrONT Documentation: https://culebront-pipeline.readthedocs.io/en/latest/
- BaseDmux GitHub Repository: https://github.com/vibaotram/baseDmux
- Snakemake Documentation: https://snakemake.readthedocs.io
- Singularity Documentation: https://sylabs.io/docs/
- CulebrONT PyPi Downloads: https://pypi.org/project/culebrONT
Note: CulebrONT is licensed under CeCill-C and GPLv3. Intellectual property belongs to IRD, CIRAD, and the authors.
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