KY INBRE Essential Bioinformatics Workshop 2025

The UK/UofL/KY INBRE Essential Bioinformatics Workshop provides a ground-level introduction to analysis of next generation sequence (NGS) data using open source command line tools. 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 and the University of Louisville. The goal of the workshop is to provide participants with valuable experience in using industry-standard bioinformatics tools for genomic data analysis. No prior experience with the unix/linux command line or NGS data analysis is required but it is essential that all applicants have a good understanding of DNA/RNA/protein biology, gene structure and expression.

The following topics will be covered (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 (FastQC, 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 (HISAT2, StringTie, CuffDiff)

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