In coordination with the Health Sciences Center (HSC), the Utah Center for Genetic Discovery (UCGD), and Huntsman Cancer Institute (HCI), the Bioinformatic Analysis Shared Resource has been renamed the HCI Cancer Bioinformatics (CBI) Shared Resource.
CBI provides four services related to the processing and interpretation of next-generation sequencing experiments: consultation, analysis, infrastructure, and translational omics. These services are tailored for cancer-related projects and available to any University of Utah researcher.
CBI 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 or submit a help request.
A second key function of CBI 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 workflows for all of the major classes of next-generation-sequencing applications (ChIPSeq, MethylSeq, RNASeq, Single Cell, and Germline-Somatic Variant Identification).
A third key service of CBI is to facilitate genomic experimentation and bioinformatic analysis by investing heavily in developing and maintaining a variety of compute infrastructure services, software tool kits, and containerized workflows. See CBI's GitHub Repository. This is divided into three parts.
Illumina Sequence Processing
We work jointly with the High-Throughput Genomics (HTG) Shared Resource 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.
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.
A number of custom software packages are developed and maintained by members of CBI 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 research is a final service provided by CBI. 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 Tempus, Caris, Foundation Medicine and from HCI-affiliated consortia, including the ORIEN AVATAR tumor normal exome project. See Translational Omics for more information.