CHG Bioinformatics and Statistics Core
Our Core boasts a high-performance computing (HPC) cluster, “Secretariat,” with diverse nodes optimized for general purpose, big memory, interactive and GPU-intensive tasks. The Core team offers dedicated support with statistical experimental design, data analysis, pipeline development and statistical interpretation, making it an essential partner for researchers navigating complex genomic and multi-omics datasets.
CHG Bioinformatics and Statistics Core
Our Core boasts a high-performance computing (HPC) cluster, “Secretariat,” with diverse nodes optimized for general purpose, big memory, interactive and GPU-intensive tasks. The Core team offers dedicated support with statistical experimental design, data analysis, pipeline development and statistical interpretation, making it an essential partner for researchers navigating complex genomic and multi-omics datasets.
Meet the Bioinformatics and Statistics Core
Dr. Vijay Shankar (pictured right) directs the Clemson University Center for Human Genetics Bioinformatics and Statistics Core. Ms. Maria Adonay (pictured center) serves as a Bioinformatician in the Core. Dr. John Poole (pictured left) serves as a Bioinformatician/Programmer in the Core. Combined, they hold a total of more than 20 years of bioinformatics and statistics experience!
Our Core provides comprehensive services for transcriptomics, genetics and genomic analyses, epigenetics and statistics. We are happy to consult with you about your project, and help design your experiment!
Equipment
GPU Computing
We have a series of GPU computing resources on our cluster which include a NVIDIA DGX-A100, H100NVL nodes and L40S nodes. These play critical roles in hyper-parallelism for computational acceleration and ML/DL-based AI workflows.
Petabyte Scale Data Storage
The enterprise-grade storage solution on our cluster is enabled by the flexible and scalable Dell PowerVault ME architecture. The PowerVaults are connected to storage hosts through dual-redundant high speed 12GB SAS. The PowerVaults are configured under RAID6 for two-drive failure at each volume group.
High Density Computing
We have maximized our compute performance within limited rack space by implementing and investing in ultra-high density computational frameworks such as the 2U C6400 and C6600 units. These house multiple compute nodes within each chassis and allow for flexible customization of compute hardware.
Data Stored on Secretariat
CPU Core Hours Used on Secretariat in 2025
Number of Labs Currently Serviced by Secretariat
Services
Bulk Transcriptomics
Our core offers comprehensive end-to-end analysis and interpretation for reference-based and de novo whole and targeted transcriptomes. We can also customize the workflows based on the experimental design and biological questions.
Single-Cell/Nuclei Transcriptomics
We offer a well-established gold standard analysis workflow for processing single cell/nuclei transcriptomic and multi-assay data from quality control to cell type annotation, differential expression testing and network-based analyses.
Genetic Variant Analysis
Our core is able to offer an ultra-high throughput, GPU-accelerated variant calling analysis framework which includes short nucleotide and structural variants as well as variant annotation for a range of project sizes, from small cohorts, all the way to population-scale datasets.
Network-based Statistical Analyses
Our core statisticians are able to enhance your analysis insights by adding network-based analysis to your project workflow. These include co-expression and co-occurrence analyses, interaction-based networks, and network topology- and index-based comparison analyses.
GWAS & TWAS
Our team of statistical geneticists are able to offer our univariate and multivariate genome and transcriptome wide association analyses as custom workflows. These workflows also include variant annotation and interpretation.
Microbiome Community & Functional Analysis
We offer analysis workflows for community profiling of 16S/18S/ITS data through QIIME and QIIME2, functional profiling of shotgun metagenomics data through HUMAnN, and microbial gene-expression profiling of meta-transcriptomic data through MG-RAST and MetaTrans.
Whole Genome Assembly & Annotation
We offer a series of pipelines for reference-based and de novo genome assembly and annotation from short read, long read and hybrid sequencing approaches. We also are able to build pangenome workflows for reference panels and population-scale whole genome sequencing data.
Population Genetics
Our core’s population genetics workflow include analyses such as phylogenetics, population structure characterization and stratification, and calculation of population genetic parameters.
Epigenetics
We have standardized workflows for ATAC- and ChIP-seq that we can offer as service. We can also build customized workflows for DNA methylation and chromatin conformation (HiC) data.
Statistical Consultation
Our team of statisticians and bioinformatics are able to assist in the aspects of your projects such as experimental design, statistical power calculation, exploratory analyses, data-driven hypothesis generation and statistical formalization of biological questions. We can also develop new statistical approaches to address your project-specific questions.
Connect with Our Experts
Ready to explore how our Bioinformatics and Statistics Core can benefit your research? Reach out today to schedule a consultation with our team and discover the possibilities.
Questions?
For further information about the Clemson Center for Human Genetics please contact us.
or
chg@clemson.edu