Genomics & Bioinformatics Core Facility

Bioinformatics

The Bioinformatics Core Facility is designed to provide services and resources that will assist the Notre Dame Research community from project development through publication. Our analysts work to identify appropriate experimental design, provide guidance for data processing and analysis of genomic datasets, and advise how to archive your results.

Areas of Support

  • Genomic sequence data analysis (areas include RNAseq, small RNA, whole genome sequencing, RADtag analysis, ChIP-seq, FAIRE-seq, and more...)
  • Consultation on study design
  • Specification of appropriate software tools and methods
  • Education and Training
  • Bioinformatic tools and software development
  • Letters of support to secure research funding
  • Access to biocomputing resources

NGS Data Analysis

We provide data analysis for a number of sequencing technologies, including RNA-Seq, small RNA, whole genome sequencing, Restriction digest Associated DNA sequencing (RAD-tag/RAD-seq), ChIP-seq, and more. We recommend contacting us for an initial consultation; especially in the early phases of project development. During the consultation, we will discuss sample types and replicate numbers needed for your experimental design, types of analyses possible, expected data files, and expected turn around time. 

Data Files

Results from analyses will be accessible for download via a secure location upon analysis completion.

Service Rates

Notre Dame affiliated labs and colleagues at Indiana CTSI institutions receive internal service rates. A different service rate is applied to external users. For inquiries about external service rates, please contact us.

Consultation and Office Hours

Please contact Joseph Sarro, Senior Analyst, to make an appointment or visit during scheduled office hours.

Joseph Sarro, Ph.D. Senior Analyst
Bioinformatics Office 109 Galvin Life Science Center
Phone Number (574) 631-1217
Office Hours  Please contact

Data Storage

Data will be backed up by the GBCF for a period of six months. File storage will consist of raw data as well as data files generated during analysis. Please take measures to back up your data following completion of analysis.

Available Software

These software packages are licensed by the University and available to ND researchers. If you have any questions, contact Joseph Sarro, Senior Analyst, for more details and information.

  • MetaCore Pathway Analysis – Integrated software suite for functional analysis of Next-Gen Sequencing, variant, CNV, microarray, metabolic, SAGE, proteomics, siRNA, miRNA, and screening data
  • Ingenuity Pathway Analysis – Web based software application for the analyis, integration, and interpretation of data derived from gene, transcript, and protein expression data
  • Sequencher – DNA sequence assembly software for windows
    • Must be connected to the Notre Dame network
    • Must have KeyAccess software installed

Available Biomodules

The core, in conjunction with the CRC, has added new biomodules to the CRC. The module currently contains twelve pieces of software; FastQC, Trimmomatic, Bismark, BWA, Bowtie-2, TopHat, Samtools, GATK, Picard tools, Trinity, HTSeq, and Cutadapt. All of this software can be accessed with the command “module load bio” on the command line when logged into the CRC. For more information on these tools, please access the wiki page here: http://wiki.crc.nd.edu/wiki/index.php/Installed_Applications#Biology 

Questions on usage or requests for additional software can be directed to Joe Sarro (jsarro@nd.edu)

Center for Research Computing (CRC) Resources

The CRC houses two complementary resources: the High Performance Computing section, providing over 20,000 cores of computational power with the associated support infrastructure for both hardware and installed software, and the Cyberinfrastructure section, empowering Faculty and industry partners to develop research environments that support advanced data and information processing services including acquisition, storage, management, integration, mining and visualization of data.

CRC Research Overview

The foundation of the CRC is a state of the art High Performance Computing (HPC) facility providing advanced research computing support to the Notre Dame community. Building on this foundation, the Cyberinfrastructure (CI) group was established to empower faculty and industry partners to develop research environments that support advanced data and information processing services, including acquisition, storage, management, integration, mining and visualization of data. Together, HPC and CI bring a broad range of capabilities to partnerships with researchers at Notre Dame and beyond.

Learn more about the CRC research focus areas by exploring their website, and contact CRC if you may be interested in working with them. They offer a combination of free services and work for hire, and partner with researchers on grant proposals to fund new projects.