The bioinformatics core 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. The bioinformatics core also has developed a number of custom scripts to facilitate microbiome data processing with a standard pipeline. If you would like to run the core'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, send an email to our Request Tracker, bioinformaticshelp@bio.hci.utah.edu


Contact Us

Bioinformatic Analysis Director
David Nix, PhD

Bioinformatic Analysis Associate Director
Timothy Parnell, PhD


HCI Senior Director Oversight
Alana Welm, PhD

Faculty Advisory Committee Chair
Katherine Varley, PhD

Faculty Advisory Committee Members
Richard Clark, PhD
Jason Gertz, PhD
Christopher Gregg, PhD
Mei Koh, PhD
Philip Moos, PhD
Andrew Post, MD, PhD
Sean Tavtigian, PhD
Joseph Yost, PhD