Bioinformatics for Bacterial Genomics & Metagenomics Workshop
Travel
Location ARC-Biotechnology Platform, Pretoria, South Africa
Date March 18-22, 2024
Participants are chosen through an application process. Apply Now!! Applications are due by February 9, 2024
Travel grants will be considered for international participants.
Workshop Overview:
This workshop provides biologists and bioinformatics participants with an introduction to genomic epidemiology. The course will take students from raw metagenome sequence data isolated from Brucella samples through assembling a phylogenetic tree. The topics include sequencing approaches, sequence read processing (QC, trimming), genome assembly and alignments, genome annotation, taxonomic assignment of metagenome sequence data, and building a phylogenetic tree to understand the relationships among samples. The entirety of the training will use an online tool called kbase, which is a software and data science platform intended to make complex tasks in genomics accessible to scientists that lack either the tools and/or specialized skill sets.
Learning Objectives:
By the end of the course, participants should be familiar with content from the following:
Topic 1: Introduction to Next-Generation Sequencing
• Sequencing platforms and their relative strengths and drawbacks
• Sequence data formats (e.g. fastq, fasta) and types (single, paired, long vs. short read)
Topic 2: Sequence quality
• Assessing the quality of the read data
• Removing low quality bases
• Adapter trimming
• Contamination detection
Topic 3: KBase
• Creating an account
• Navigating the system
• Uploading data
• Getting help
Topic 4: Genome Assembly and Annotation
• What is an assembly?
• Assembling whole genome data vs. whole metagenome data
• Tools for assembling genome
• Using SPAdes to assemble whole metagenome data in KBase
• Evaluating the assembly
• Annotation of Bacterial Genomes: What is it and what tools are available
• Annotating whole metagenomes in KBase using Prokka
Topic 5: Taxonomic Assignment and Constructing a Phylogenetic Tree with Brucella
• Background on taxonomy assignments, databases, tools
• Assigning taxonomy with KBase using GTDB-Tk
• Phylogenetics and its role in genomic epidemiology
• General overview of Brucella and brucellosis
• Types of data used to build phylogenetic trees and their relative strengths and weaknesses (e.g. MLST, MLVA, Sanger, Next-Generation sequence data)
• Interpreting a phylogenetic tree
Send all inquiries to vhardy@cvm.tamu.edu
