Next Generation Sequencing Workshop

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)

 

Learn more: https://www.kyinbre.org/cores/genomics-training-and-education-center/ngs23



Sponsored by NIH-KY INBRE