Microbiome Helper started as a Github repository that contained several resources to help researchers working with microbial sequencing data:
- A series of scripts that help process and automate various microbiome and metagenomic bioinformatic tools.
- Workflows or standard operating procedures (SOPs) for analyzing 16S/18S/ITS marker gene and metagenomic data.
- Tutorials with test data, example output, and questions for different microbiome analyses.
- A Virtual Box image that can be used to run our workflows and tutorials with little or no configuration (note that we have now moved this to Old SOPs as they have not been updated for a while).
Microbiome analysis tools have changed substantially since Microbiome Helper was first released in 2017. We have been working on updating everything and migrating it to this website for a while now. We have completed updating the tutorials, and any of the other pages on this website that have information filled in should be working now.
It is important that you cite the tools that are wrapped by our scripts and workflows, as well as our 2017 paper:
Comeau AM, Douglas GM, Langille MGI. 2017. Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research. mSystems 2(1): e00127-16; DOI: 10.1128/mSystems.00127-16
