Bioinformatics

The YCGA Bioinformatics Core, with seven Ph.D. level scientists, provides next-generation sequencing (NGS) analysis services and analysis tools to YCGA customers and the Yale community. The group has developed best practice analysis pipelines for germline and somatic whole-exome sequencing (WES), whole-genome sequencing (WGS), bulk RNA-seq, single cell RNA-seq, microRNA-seq, ChIP-seq, methyl-Seq, ATAC-seq, sgRNA-seq, 4C-seq, Hi-C, CyToF, spatial transcriptomics, whole genome and transcriptome assembly and 16S/18S metagenomics, and have extensive experience with Illumina, Ion Torrent, 10x Genomics, PacBio and Oxford Nanopore sequencing. They perform bioinformatic analyses, work with Yale investigators to develop new NGS applications and tools, and provide visualizations and writeups for journal manuscript submissions and grant applications.

Our bioinformatics charges reflect a combination of the effort required to perform the analysis and the amount of data involved. We have two basic charging units, an "Analysis - Small Batch" charge of $607 for Yale investigators ($795 for external customers) and an "Analysis – Large Batch" charges of $441 for Yale investigators ($579 for external customers) for large datasets, depending on the application:

• Amplicon sequencing, sgRNA and equivalent small panels
  • Small Batch: up to 100 samples
  • Large Batch: each add'l 500 samples
• Exomes, bulk RNA-seq, ChIP-seq, capture-based datasets and bacterial/small whole-genome data
  • Small Batch: up to 20 samples
  • Large Batch: each add'l 100 samples
• Large whole-genome datasets (WGS, Hi-C, whole genome methylation)
  • Small Batch: up to 10 samples
  • Large Batch: each add'l 50 samples
• Single-cell datasets, CyToF
  • Small Batch: up to 5 samples
  • Large Batch: each add'l 25 samples

For other bioinformatics effort that does not involve data analysis (report customization efforts, transfer of non-YCGA sequencing data, data deposition to SRA/GEO/…), a 0.5 unit Small Batch charge will apply. For larger efforts, we can provide estimates of the charges involved, or can provide full bioinformatics support for your lab as a percentage effort, for as many or few months as you require.

If you need help with analyzing sequence data, please contact Dr. Sameet Mehta.

Dr. Francesc Lopez provides analysis services to Yale Cancer Center members at no cost. YCC members should contact him at francesc.lopez@yale.edu. Dr. Dejian Zhao provides analysis services to Yale Liver Center members at no cost. YLC members should contact him at dejian.zhao@yale.edu.