UK/UofL/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 (www.kyinbre.org) 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.
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Workshop sessions will be held on the UK and UofL campuses from 9 am to 5 pm from Monday, July 14 to Thursday, July 17). Participants from Lexington, Louisville and their environs, are expect 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 e-mail once your application is accepted.

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

Email *
Name *
Affiliation *
Applicant educational background
Please provide information on your primary education and degrees (if applicable), as well as relevant experience in bioinformatics/computer sciences.
Education *
Your college degrees, additional training, and any other relevant educational background
Current research interests. Please provide information about the type of research in which you are currently involved.
 *
Relevant bioinformatics experience *
Please provide information about any prior experience you have working in the command line environment, analyzing DNA/RNA sequence data with various bioinformatic tools (blast, genome assembly, RNAseq analysis, metagenomics, etc.)
Reason for interest in the workshop. Please note that applications always exceed available spots and we try to offer positions to individuals who have an immediate need for bioinformatics skills, or expect to do so in the near future.
 *
If your application is accepted, do you expect to attend the workshop in person or remotely? *
Additional background
Please provide any additional information that you would like to be taken into consideration in the evaluation of you application.
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