ASM2018: Genomics Workshop

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Introduction

This workshop presents practical guidelines for interpreting whole genome sequence (WGS) data from bacterial pathogens. We will focus on how WGS can be applied to investigate suspected outbreaks, especially those caused by food-borne disease-causing bacteria. Strategies for using Illumina, PacBio and Nanopore platforms will be introduced along with direct metagenomic sequencing of clinical samples. We will include an interactive session on using freely available cloud-based platforms for undertaking applied bacterial genomics analysis. Although targeted at Food Safety, Public Health or Clinical microbiologists this workshop will be of interest to anyone seeking practical strategies and tools that they can use to investigate their own bacterial WGS data.

This page contains information required for you to access Galaxy Australia and to self-navigate through a number of tutorials to explore:

  • Bacterial genome assembly from WGS data (core)
  • Gene annotation of your assembled genome (core)
  • Variant detection on your assembled genome (core)
  • Antibiotic resistance gene detection (optional)
  • MLST typing (optional)
  • Plus additional support tutorials for Galaxy Australia access and Key Tasks (core)

Background

Prior to attending the workshop it is the expectation that you will work through the core tutorials. The optional tutorials will be covered on the day but are not required to be completed prior to the day.

The workshop will also focus on:

  1. The benefits of chaining tools together into executable workflows
  2. Exporting of data (sequence, tables, visualisations, etc) for use downstream of the Galaxy Australia environment

Accessing Galaxy Australia

  1. Galaxy Australia
  2. Use your academic or professional email to register, follow the Get Started tutorial
  3. Complete the Learn Key Tasks tutorial. The features explored here will be used in the following tutorials.
  4. Bacterial genome assembly from WGS data (core)
  5. Gene annotation of your assembled genome (core)
  6. Variant detection on your assembled genome (core)
  7. Antibiotic resistance gene detection (optional)
  8. MLST typing (optional)

Feedback

We ask that prior to the workshop you also complete the survey below. It will prompt you with questions regarding the tutorials and any further questions on the process or outputs you have. These will be compiled into a FAQ and presented at the workshop.

Complete Survey