Genomics Training Workshop

The Essentials of Next Generation Sequencing Workshop, NGS ’22, offers an introduction to applied bioinformatics. The Workshop is supported by funding from KY INBRE and is organized through a collaboration between the Departments of Plant Pathology and Computer Science at the University of Kentucky, the University of Louisville, and Eastern Kentucky University. The goal of the Workshop is to introduce participants to the use of common (and open source) tools for data analysis (genomic, RNAseq). No prior experience or background in NGS is required, but it is essential that all applicants have a good understanding of DNA/RNA/protein biology, gene structure and expression.

Please note: based on previous participants’ feedback, this will be an abbreviated offering that will include the following topics (programs to be used are listed in parentheses):

    1. Working in the UNIX/LINUX command line environment
    2. Assessment of sequence quality and trimming of poor quality reads (fastQ, Trimmomatic)
    3. Genome assembly from short sequence reads (VelvetAdvisor, Velvet, VelvetOptimiser)
    4. Aligning sequence reads to a reference genome (HISAT)
    5. Identifying sequence variants (mpileup, vcftools, bcftools)
    6. Gene prediction (SNAP, AUGUSTUS, MAKER)
    7. Genome browser (Integrated Genomics Viewer)
    8. Differential gene expression analysis (StringTie)

Note: We will NOT cover metagenomics analysis in this workshop but can provide a training module that participants can work through on their own.

The Workshop will be run from 9 am to 5 pm, Monday to Thursday, June 27-30 (with breaks for coffee and lunch). It is essential that participants attend all day, every day, because missed sessions will negatively impact subsequent activities. It will be delivered in an online format (with a possibility of attendance at a local training center in Lexington, Louisville and Richmond), and it is essential that participants will have access to following:

    • Administrator privileges to a recent model laptop/desktop computer
    • Stable, hi-speed internet connection

Participation in the workshop is free to individuals associated with educational institutions in Kentucky and other IDeA states. The number of spaces available is limited, so please apply asap! You will be informed by email once your application is accepted.

Presented by the KY INBRE Electron Microscopy Cores located at:


Click here to apply for Workshop

If you have any questions about the workshop or about this application form, please contact Dr. Mark Farman at