Home

Welcome to the MAPT Wiki. This is the home page, and provides a sort of home-base for viewing documentation. The sidebar (to the right) is always available, no matter which page you navigate to.

This page should get you up-and-running for this pipeline

Naming

This has been my most notable, and in-depth, project to date. As a result, I feel it should have a proper name. Due to the nature of this project revolving around mapping noisy microbial reads (hopefully) down to the species level, the following name seemed appropriate: Microbial Automated Processing Tool, or MAPT for short.

Getting Started

• Usage: General usage of the pipeline and links to the software used
• Installation: How to install the pipeline
• Parameters & Configuration Files: Explanation of the config.yaml file that holds your settings
• Running the Pipeline: How to execute the pipeline
• Updating the Pipeline: How to update the pipeline
• Running Guppy in a Singularity Container: How to run guppy outside the pipeline, if you would like to do so
• Example SLURM Scripts: SLURM Scripts to get you started on SciNet
• Sample Data: A series tutorials about what to expect with the pipeline to ensure you are set up properly
  • Expected Outcomes
  • Potential Errors
• Notes to Future Maintainers: Notes to those that may be maintaining this pipeline in the future

Support

If you need help, have questions, or have feature ideas please open a new issue