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Microbiome Helper is a repository that contains 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 rRNA 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 to Microbiome Helper 2 for a while now, and you can see all of the workflows that are included in this as well as how they all fit together here. If you would prefer to use the original Microbiome Helper workflows, they can be found here.

You can use the sidebar menu to navigate the wiki.

Note that the scripts and workflows are continually being updated.

These scripts were produced by the Integrated Microbiome Resource. It is important that you cite the tools that are wrapped by our scripts. Also, our paper on Microbiome Helper has been published in mSystems. Please cite this paper if you use our repository:

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

All older scripts (prior to February 2020) can be found in the v1.0 release here.