KY INBRE Essentials of Next Generation Sequencing Workshop 2023

Page updated May 19, 2023

The Essentials of Next Generation Sequencing Workshop, NGS ’23, offers an introduction to applied bioinformatics. The workshop is supported by funding from Kentucky IDeA Networks of Biomedical Research Excellence (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)

Workshop sessions will be held on the UK and UofL campuses from 9 am to 5 pm from Tuesday, June 20 to Friday, June 23 (with breaks for coffee and lunch). Participants from Lexington, Louisville or their environs, are expected to attend in person, and it is essential that participants attend ALL DAY, EVERY DAY, because missed sessions will negatively impact subsequent activities. Individuals associated with institutions >50 miles from Lexington or Louisville will be able to attend remotely but will have a much better experience if they attend in person. Depending on needs, KY INBRE may be able to cover costs of accommodation. (Apologies, but we will not be able to cover expenses this year.)

It is essential that participants will have access to following:

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 a collaboration between KY INBRE and:



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