KY INBRE Essentials of Next Generation Sequencing Workshop 2024
The UK/UofL/KY INBRE Essentials of Next Generation Sequencing Workshop, provides a ground-level introduction to analysis of Next Generation Sequence data using the command line interface. 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 introduce participants to the use of common (and open source) tools for data analysis (genomic, RNAseq). No prior experience with the unix 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):
Working in the UNIX/LINUX command line environment
Assessment of sequence quality and trimming of poor quality reads (FastQC, Trimmomatic)
Genome assembly from short sequence reads (VelvetAdvisor, Velvet, VelvetOptimiser)
Aligning sequence reads to a reference genome (HISAT)
Identifying sequence variants (mpileup, vcftools, bcftools)
Gene prediction (SNAP, AUGUSTUS, MAKER)
Genome browser (Integrated Genomics Viewer)
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.
Workshop sessions will be held on the UK and UofL campuses from 9 am to 5 pm from Monday, July 22 to Thursday, July 25 (lunch and coffee will be provided). Participants from Lexington, Louisville and 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.
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, but the number of spaces available is limited, so please apply promptly. You will be informed by email once your application is accepted.
Presented by a collaboration between KY INBRE and:
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If you have any questions about the workshop or about this application form, please contact Dr. Mark Farman at farman@uky.edu.
