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The Cancer Bioinformatics (CBI) Shared Resource supports and maintains pipelines for 16S,metagenome and metatranscriptome analysis of microbiome data. We can also assist with additional types of community analysis from 16S and metagenome sequencing including quality control, alignment, taxonomic classification, functional analysis, statistical associations with clinical outcomes and visualizations.


The existing pipelines are written in nextflow with singularity and are designed to run at CHPC using slurm and currently support paired end reads. All the heavy lifting apps needed to run the pipeline are already installed in the singularity container. CBI also has developed a number of custom scripts to facilitate microbiome data processing with a standard pipeline. If you would like to run CBI's microbiome pipelines yourself on CHPC, you only need to:

  • Download the custom scripts and put them in your path;
  • Download the scripts in microbiomeSingularityPipeline and put all the scripts in your working directory;
  • Follow the instrucitons on github page to set up jobs

16S rRNA - Microbial community analysis using QIIME2

Metagenome - Functional analysis using HUMAnN2

Metatranscriptome - Functional analysis of paired metagenome and metatranscriptome data using HUMAnN2

If you would like assistance with your Microbiome analysis, email our Request Tracker.

Microbiome Illustration