Genomics Resource Center - Analysis Services

Each analysis project is performed in close consultation with the researcher

Using a team of experienced software engineers, bioinformatics analysts, and biologists, the GRC provides a range of genomic data assembly and analysis services using state-of-the-art software pipelines and the IGS computational infrastructure. Many of these services are provided in conjunction with our colleagues in the IGS Informatics Resource Center. We have deployed a hierarchical data storage system and high-capacity compute grid to support large data analysis projects. Our analysis services can be used alone or in combination with our laboratory services to provide comprehensive data generation and analysis for your project. Each analysis project is performed in close consultation with the researcher to ensure that the analysis targets the scientific question at hand. Analysis results are delivered via Aspera file transfer, hard media, or NCBI deposit. Services are provided on a fee-for-service basis and each project is customized to the needs of the investigator.

For more information or to discuss your research needs, please contact the GRC.

Genomic and Metagenomic Sequence Assembly

Using a range of sequence assembly tools tuned to the appropriate genome size and characteristics, we produce an optimized assembly and deliver contigs, scaffolds, and metrics in a variety of standard formats.

Comparative Genome Assembly

Given a reference sequence, data is aligned and assembled against the reference. Resulting contigs, scaffolds, and variant records are delivered.

Genome Annotation

We provide both automated and manual annotation of prokaryotic and eukaryotic genome sequences.

Transcriptome Analysis

Transcriptome (RNA-Seq) data can be analyzed to determine gene or isoform level expression profiles, sequence variantion, and differential expression between multiple conditions and/or timepoints.

Epigenomic Analysis

We analyze ChIP-Seq, BS-Seq, PacBio base modification, and other types of epigenomic data. Data from ChIP-Seq experiments are aligned to a reference genome and analyzed for peak enrichment to identify DNA-protein binding sites. Differential peak analysis between experiments can be used to identify binding sites specific to certain conditions or proteins. For BS-Seq experiments, DNA methylation patterns are detected by aligning sequence data derived from bisulfite-treated DNA (BS-Seq) to both a reference genome and a version of the reference genome that has been in silico bisulfite converted. This dual alignment analysis enables more accurate identification of methylated sites and their boundaries. PacBio's unique SMRT Sequencing method enables direct detection of methylation and other DNA modifications by measuring kinetic variation during nucleotide incorporation by the polymerase. Detailed base modification motif reports are generated.

Variant Detection and Annotation

Using analysis pipelines developed specifically for variant detection, sequence data is aligned to available reference sequences. SNPs, indels (insertions and deletions), and structural variants are detected, quality-filtered, and annotated (coding, non-coding, synonymous, non-synonymous, etc.). In order to identify novel or rare variants, the variants are compared to an in-house database of known variants that includes the latest dbSNP and 1000Genomes data as well as other known variants from multiple organisms. Data visualization tools are available to browse the results. Comparative analysis of variants calls is also available.

Pathway & Network Analysis

Given a set of variant positions, genes, or other loci associated with a particular phenotype, we use software packages, including Ingenuity Pathway Analysis (IPA), developed specifically to analyze gene pathways and networks to find associations with functional profiles, tissue or disease specific biomarkers, and other genes in the same pathways and networks. We also use open-source network and visualization tools DAVID, Cytoscape, and Reactome to complement network/pathway analysis to increase the accuracy and sensitivity of network/biomarker identification.

Custom Data Analysis

Our computational infrastructure and expertise enables cutting-edge custom analysis for a broad range of genomics applications. We will customize an analysis plan for each project in close consultation with each investigator. Please contact the GRC to discuss custom analysis projects.

Sequence Data Storage and Distribution

Our hierarchical data storage system provides both high-performance, grid-attached storage for computational analysis as well as long term, cost-effective data storage. Data can be distributed via FTP, Aspera file transfer, hard media, and NCBI deposit.