We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Microbiome Helper is a repository that contains several resources to help researchers working with microbial sequencing data:
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.
Amplicon SOP v2 (virtual box workflow)
Amplicon SOP v2 (qiime2-2022.11)
PacBio Amplicon SOP v2 (qiime2-2022.2)
Metagenomics SOP v2
Metagenomics SOP v3
Wet-Lab SOPs on Protocols.io
Microbiome for beginners
mSystems paper data