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Workshop: Wet Lab and Computational Analysis

October 3 - October 15

Next month, our NextGen Sequencing and Bioinformatics cores are collaborating with the Health Sciences Library.  They will offer a 4-part workshop on Next-Generation Sequencing and related analysis. Two sessions will be devoted to the wet-lab side of Next-Gen Sequencing, and two about the computational analysis of the results. Each session is 1hr and 15 minutes, and they’ll take place in the new computer lab at UF Health Science Center Libraries (room c1-21). The workshop schedule and class description:

 

NEXT GENERATION SEQUENCING (NGS) PART 1: BASIC EXPERIMENTAL WORKFLOW

WHEN:10/3, 10:30am – 11:45am

INSTRUCTOR: David Moraga (moraga@ufl.edu)

PRE-REQUISITES:  NONE

This workshop serves as an introduction to the basic workflow of DNA sequencing using next generation technology.  All students, faculty, and research staff in life sciences research interested in NGS in their work should attend. Topics will include:

  • Basics of DNA sequencing
  • Applications where NGS can be used (i.e. Genomics, epi-genomics, transcriptomics, etc.)
  • Sample preparation including library construction (adapters, barcodes)
  • Chemistry behind NGS
  • Single versus pair-end reads
  • Image analysis and base calling
  • Services offered at ICBR
  • Instruments available at ICBR (limitations to the instruments, how to determine which one to use, read length capabilities)

 

NEXT GENERATION SEQUENCING (NGS) PART 2: TECHNICAL ASPECTS AND CHALLENGES

WHEN: 10/5, 10:30am – 11:45am

INSTRUCTOR: David Moraga (moraga@ufl.edu)

PRE-REQUISITES:  NONE, BUT ATTENDANCE OF NEXT GENERATION SEQUENCING PART 1 IS RECOMMENDED

This workshops serves as a continuation for those who attended next generation sequencing part 1 or those who have knowledge of the basic steps of NGS.  Here, we will focus on the technical aspects and challenges involved in NGS (i.e.  What can go wrong and how can we prevent?).  Topics will include

  • Technical and biological errors
  • Best practices for library quantification and library quality control
  • Library concentration influences on clustering
  • Library contaminations (i.e. primer-primer dimer, adapter dimer)
  • More in-depth discussion on image analysis and base calling
  • Spike-in as quality control

 

NEXT GENERATION SEQUENCING (NGS) ANALYSIS PART 1

WHEN: 10/10, 10:30am – 11:45am

INSTRUCTOR: Alberto Riva (ariva@ufl.edu)

PRE-REQUISITES:NONE, BUT FAMILIARITY WITH UNIX AND HIPERGATOR IS RECOMMENDED. 

This introductory workshop will address the basics of NGS analysis using UF Research Computing’s Unix environment (HiPerGator).  Temporary access to HiPerGator and sample dataset will be provided for those attending to follow along.  Topics will include

  • Introduction to the HiPerGator environment
  • Tools available on HiPerGator for NGS analysis
  • Explanation of various fields associated with FASTQ files and how to identify from FASTQ header
  • Basic workflow in NGS analysis including emphasis on
  • Quality check (good versus bad)

 

NEXT GENERATION SEQUENCING (NGS) ANALYSIS PART 2

WHEN: 10/15, 1:30pm – 2:45pm.

INSTRUCTOR: Alberto Riva (ariva@ufl.edu)

PRE-REQUISITES:  NONE, BUT ATTENDANCE OF NGS ANALYSIS PART 1 IS RECOMMENDED.  ALSO, FAMILIARITY WITH UNIX AND HIPERGATOR IS RECOMMENDED.  

Now that we have gained experience with navigating through HiPerGator and seen the basic workflow for NGS analysis, it is time to put everything together and get some hands-on experience.  In this workshop we will use tools available on HiPerGator to identify variants in small sample genomic sequence file.  Here we will

  • Perform quality check of the sample FASTQ file
  • Interpret quality check results
  • Trim out reads accordingly
  • Read assembly
  • Variant calling

 

To register, visit myTraining page. Registration is free but required. The easiest way to find these courses in myTraining is to search for the keyword “UFH_HSCLNGS.” If you have any questions or would like more details, please contact the Bioinformatics core – ICBR-Bioinformatics@ad.ufl.edu

Details

Start:
October 3
End:
October 15

Organizer

ICBR
Phone:
(352) 273-8030
Email:
ICBR-ContactUs@ad.ufl.edu
Website:
www.biotech.ufl.edu