In partnership with the Institute for Precision Medicine, the Molecular Biology Information Service of the Pitt Health Sciences Library is pleased to provide University of Pittsburgh researchers free access to the CLC genomics workbench from QIAGEN as well as the CLC BioMedical Workbench, Ingenuity Pathway analysis and Ingenuity Variant analysis for analysis of next generation sequencing (NGS) datasets. Monthly workshops are offered in the application of these tools as well as assistance by analysts from the Department of Biomedical Informatics Genome Analysis Core (DBMI-GAC).


The growth of genomic sequencing has placed an incredible burden on bioinformatics support. The use of bioinformatics core personnel is key, however, the model is not sustainable and general lab researchers need to be educated to perform their own bioinformatics (at least simple low level analyses). Towards this goal, IPM has worked with the Molecular Biology Information Service of the Health Sciences Library System to financially support the procurement and deployment of the CLC Genomics Workbench from QIAGEN. This software has a simple windows user interface that can be readily used by wet lab researchers, and streamlines analysis of Next Generation Sequencing (NGS) datasets such as RNA-Seq, Exome Sequencing, and ChIP-Seq. Given that (1) the analytical workflows for this software suite are complex and (2) the emphasis on rigor and reproducibility in data analysis is increasing, HSLS-MBIS collaborates with the Genomics Analysis Core of the Department of Biomedical Informatics (DBMI-GAC) to provide comprehensive assistance with the use of CLC Genomics Workbench for the analysis of NGS data.

Through educational series, investigators are exposed to data preparation, data importation, and CLC Genomics Workbench software capabilities via an in-depth, 3-hour monthly workshop offered by HSLS-MBIS. If additional guidance is needed, investigators may receive up to 5 hours of free, individualized assistance for CLC Genomics Workbench-related data analysis provided by a DBMI-GAC analyst. Prerequisites are workshop attendance and completion of an online questionnaire about the specific project. If necessary, the DBMI-GAC analyst may continue to provide further support on a fee-for-service basis. HSLS-MBIS and the DBMI-GAC analyst provide instruction and consultation in how to use CLC Genomics Workbench software, including best practices, and advice on software parameter settings appropriate to the specific project. MBIS do not engage in interpretive consultation and do not perform the analysis for the user.