Workshop Description (Intermediate Course)

The workshop will mainly focus on teaching the fundamentals of bacterial genomics and basic bioinformatics analysis. As a sample data Vibrio cholerae genome will be used as the practice dataset, and workshop participants will try to reproduce the expected results. The workshop will start with detailed instructions on how to quality control the raw sequence data and the assemble of a genome. Next, basic statistics will be explained to learn how to check the quality of assembledgenome (e.g., N50, # of contigs, # of core genes). On the genome analysis, average nucleotide identity (ANI) will be performed to identify the genome into known species followed by a prediction of open reading frames (ORFs), protein annotation, and comparing the results with other genomes.

Workshop Materials

Genome assembly

  • Quality control Illumina raw data
  • Genome Assembly by SPAdes
  • How to measure the quality of the assembled genome

Taxonomy identification

  •       A brief history of bacterial taxonomy
  • Type strain
  •       Average nucleotide identity
  •       Reference Database (EzBioCloud, NCBI)
  • Phylogenetic tree inference

Comparative genomics analysis

  • Genome annotation by Prokka
  • Search specific gene of interest by BLAST
  • How to find specific types of features (Antibiotic resistance gens, virulence factors)
  • Genome browser (Artemis)
  • Pan & core genome (Roary)
  • Visualization tools (BRIG)

Technical Requirements

  • Attendees are required to have a Hoffman2 account
  • Chrome or Firefox Internet Browser is recommended.

Instructor

Dr. Daniel (Sung-min) Ha is a Postdoctoral Fellow at the Xia Yang Lab in the Department of Integrative Biology and Physiology. Dr. Ha research focuses on Bacterial Genomics and Epidemiology and interest involves host-microbiome interaction using multi-omics systems biology approach. He earned a Bachelor in Mathematics and Genetics & Biotechnology at the University of Toronto in Canada, and a Ph.D. at Seoul National University in South Korea.

Videos

Reviews

Workshop Details

Prerequisites: Attendees are advised to take W1. Intro to UNIX command line, W2. Using NGS analysis tools prior to this workshop, but not mandatory.
Length: 3 days, 3 hrs per day
Level: Intermediate
Location: ZOOM
Seats Available: N/A

Spring 2021 Dates

Apr. 27, 28, and 29
1:30 PM-4:30 PM

REGISTRATION IS OPEN!