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Welcome to the meTAline wiki!

This resource is designed to guide you through the setup, execution, and optimization of meTAline, a Snakemake pipeline tailored for comprehensive metagenomic analysis. Whether you're a researcher, bioinformatician, or enthusiast delving into metagenomics, this wiki provides detailed instructions and insights to facilitate your journey.

About meTAline

meTAline streamlines the preprocessing of short-read metagenomic data. Its workflow encompasses:

Read Trimming and Filtering: Enhances data quality by removing low-quality sequences and adapters.

Host Read Subtraction: In case a reference genome is provided,it eliminates host-derived sequences to focus on microbial content.

Taxonomic Classification: Employs both k-mer and gene-marker approaches for microbial identification.

Functional Profiling: Analyzes the functional potential of microbial communities.

By automating these steps, meTAline ensures a consistent and reproducible analysis pipeline, saving time and reducing potential errors.

Quick Start

To get started with meTAline, refer to our Quick Start & Try-Out guide. This section provides step-by-step instructions to help you set up and execute the pipeline efficiently for a quick trial.

Deployment Options

meTAline offers flexibility in deployment to suit various computational environments:

Docker: For containerized execution, learn how to Build and Run meTAline using Docker.

Singularity: Ideal for HPC clusters, follow the guides to Build and Run meTAline with Singularity.

High-Performance Computing (HPC): For large-scale analyses, see our instructions on Running in HPC environments.

Running in HPC environment

Parallelization

To expedite processing, meTAline supports parallel execution:

HPC Cluster: Discover strategies for Parallelizing in HPC clusters.

In HPC cluster

Local Machine: Learn how to Parallelize on a local machine to leverage multi-core processors.

On local machine

Outputs and Target Rules

Understand the expected results and how to customize them:

Available Target Rules: Explore the Available target rules to tailor the pipeline to your specific needs.

Available target rules

Debugging

Want to contribute or encountered an issue? Our Debugging meTAline section offers solutions to common problems and tips for troubleshooting.

Citations and Acknowledgments

If meTAline contributes to your research, please refer to our Citations / Acknowledgments page for proper attribution and to recognize the efforts of the development team.