Accepted_test

MetaSnake is a novel framework designed to streamline bioinformatics pipeline development and data management, addressing the challenges posed by vast sequencing datasets. Integrating seamlessly with widely-used bioinformatics tools, MetaSnake is built in Python and employs an object-oriented approach with strict typing, enabling it to connect various tools and artifacts into coherent workflows.

Distinct from other workflow engines like Snakemake, MetaSnake operates at a higher abstraction level with entities such as `IlluminaSample`, `FeatureTable`, and `Assembly`. Inspired by QIIME2's artifact-centric design, MetaSnake facilitates the creation and reuse of workflows, called "recipes," which are efficiently executed using Snakemake. For comprehensive data management, MetaSnake utilizes Git for version control and Git LFS for handling large files.

The framework's capabilities are showcased through four integrated pipelines, including amplicon sequencing data processing with DADA2 and WGS metagenomics data annotation with bioBakery tools. MetaSnake also features a user-friendly API for tool integration, automatically generating command-line and graphical interfaces. The incorporation of large language models (LLMs) further enhances the framework by enabling automated workflow definition, thereby reducing manual effort.

Overall, MetaSnake lowers the barrier to entry for next-generation sequencing (NGS) data analysis, promoting reproducibility, traceability, and efficient data sharing. By leveraging existing tools and integrating advanced computational models, MetaSnake accelerates the analysis process, empowering researchers to focus more on scientific discovery and less on computational logistics.