Bioinformatic Analysis

The Bioinformatics Analysis group assists with the design and analysis of next-generation sequencing and microarray experiments. The following services are available to any University of Utah researchers.

Consultation

The Bioinformatic Analysis section provides consultation services for grant and manuscript submissions, experimental design, analysis strategy, algorithm development, and one-on-one analysis instruction. Many of our staff members have some expertise in one or several areas. Contact us to set up an appointment.

Analysis

A second key function of the Bioinformatic Analysis section involves data analysis services. This includes processing raw data to primary findings via established alignment, sample-batch quality control, and first pass group comparisons using well-developed analytic protocols for all of the major classes of next-generation-sequencing applications (ChIPSeq, MethylSeq, RNASeq, Single Cell, and Germline-Somatic Variant Identification).

You can learn more about our analysis services and recommended pipeline strategies, as well as our policies and fees for providing services.

Infrastructure Services

A third key service of the Bioinformatic Analysis section is to facilitate genomic experimentation and bioinformatic analysis by investing heavily in developing and maintaining a variety of compute infrastructure services and software tool kits. This is divided into three parts.

Illumina Sequence Processing

We work jointly with the High-Throughput Genomics core to directly process the raw data generated from Illumina sequencing. This involves processing the base level intensity files generated by the Illumina sequencers, demultiplexing the lane level data into per-sample Fastq files, and depositing the analysis-ready Fastq data into the GNomEx LIMS.

Compute Resources

To enable processing of investigators’ genomic data, we maintain numerous high-performance Linux-based compute resources, both locally in HCI as well as at the University of Utah Center for High Performance Computing (CHPC), which maintains large computing clusters with job-queue access. See Infrastructure for more details.

In addition to local resources, we have also licensed a cloud-based genomics data storage and bioinformatic from Seven Bridges.

Software Resources

A number of custom software packages are developed and maintained by members of the Bioinformatic Analysis section to facilitate the analysis of various projects. These are released as open-source code to the community. Additionally, a variety of open-source software, commercial software, and genomic reference data are maintained on the computing hardware and made available to the community. See Software for more details.

Support for Translational Genomics

Support for translational research is a final service provided by the Bioinformatic Analysis section. We have developed analysis pipelines for somatic variant detection in laboratory and patient-derived research samples, as well as samples derived in collaboration with clinical test providers such as Foundation Medicine and from HCI-affiliated consortia, including the ORIEN AVATAR tumor normal exome project. See Translational Genomics for more information.

Contact

To contact individual staff members, visit our staff page. You may also send an email to our Core, where all of the staff members will see the inquiry.

Contact Us

Bioinformatic Analysis Director
David Nix, PhD
david.nix@hci.utah.edu
801-587-4611

Bioinformatic Analysis Associate Director
Timothy Parnell, PhD
timothy.parnell@hci.utah.edu
801-587-4312

Governance

HCI Senior Director Oversight
Bradley Cairns, PhD

Faculty Advisory Committee Chair
Bradley Cairns, PhD

Faculty Advisory Committee Members
Richard Clark, PhD
Jason Gertz, PhD
Christopher Gregg, PhD
Philip Moos, PhD
Sean Tavtigian, PhD
Katherine Varley, PhD
Joseph Yost, PhD