Do you have questions about running a computational process for genomics data? Is the process new to you, or are your systems unable to process a job of this scale? We are available to help!

Computational genomics consulting is available to all faculty, staff, and students at UTIA. The consulting is offered by Dr. Matt Huff and Dr. Ryan Kuster. Combined, they bring over 10 years of experience with analysis of DNA and RNA sequence data, python and R programming, and high performance computation.

If you would like to set up a consultation, please contact mhuff10@utk.edu or rkuster@utk.edu.

The first consultation meeting is free of charge and will be used to develop a plan of action catered to your areas of need.

The hourly fee for general consultation and analysis is $80/hour (please contact us for external pricing).

Past consulting has included these topics:

• Genome or Transcriptome Assembly
• Gene Annotation
• Differential Expression Analysis
• Variant Calling (SNPs, InDels, SVs)
• Generating SSR Markers
• Small RNA Analysis
• How to Order Sequencing (Platform, Depth, Price, etc.)

If what you need isn’t on the list, we are still happy to meet with you and talk through possible support options.

• Software Installation on Linux
• Using ISAAC HPC
• R and Python Scripting
• Running containers with Singularity
• Data management and version control with Git/GitHub
• Workflow Development with Nextflow

We are excited to announce the UTIA Computational Resources, which consists of two new computers dedicated to intensive computational projects:

• Centaur (centaur.ag.utk.edu): 96 Cores, 512 Gb RAM, 200 Tb iSCSI storage.
• Sphinx (sphinx.ag.utk.edu): 64 Cores, 512 Gb RAM, 70 Tb SSD storage.

Our goal is to provide a more flexible system than what is currently available with ISAAC; you will not be required to run jobs through a scheduling system. 

We require anyone who wants to use these resources to go through an orientation presentation. Contact us at mstaton1@utk.edu or mhuff10@utk.edu to schedule your orientation. General documentation, tutorials, and FAQs can be found on our GitHub wiki. 

Courses, Workshops, and Journal Clubs

• January 2022 – RNASeq analysis – All course materials are available including recordings of sessions. If you would like to be added to the servers and follow along at your own pace, please contact Matt (mhuff10@utk.edu).
• Fall 2021, EPP 604: Journal Club Topic: Genome Evolution.
• Spring 2020, EPP 604: Journal Club Topic: RNA Sequencing.
• Fall 2020 – EPP622 Bioinformatic Applications – Full semester course, 3 credit hours, covering intro to Linux, intro to python, DNA sequence analysis for variants, RNASeq analysis for differential gene expression. All course materials are available including recordings of sessions. If you would like to be added to the servers and follow along at your own pace, please contact Meg (mstaton1@utk.edu). To be offered Fall 2022
• Fall 2019 – workshop or EPP 531, Practicing Python with Rosalind
• Summer 2019 – workshop or EPP 531, Introduction to Python

Equipment

• Wiki with computational equipment details and instructions
• FAQs about the equipment

UTIA

• UTIA OMICS Hub
• UTIA Genomics Center for the Advancement of Agriculture
• EPP 622 Bioinformatics Applications – offered Fall of even years

UTK

• OIT’s ISAAC
• CEB Bioinformatics Resource Center