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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.

These scripts were produced by the Integrated Microbiome Resource. It is important that you cite the tools that are wrapped by our scripts.

Microbiome Helper has been published in mSystems. Please cite the below paper if you use this repository:

Comeau AM, Douglas GM, Langille MGI. 2017. mSystems 2(1): e00127-16; DOI: 10.1128/mSystems.00127-16    

Note that the scripts and workflows are continually being updated.

You can use the sidebar menu to navigate the wiki.