This is a QCIF course and places are highly limited as Graduate School is paying the fee. If you are unable to attend, please de-register (or email graduateschool@uq.edu.au if you are unable to do so). An unexplained absence could result in all your future QCIF registrations becoming Waitlisted.

You will use and compare a number of popular variant detection tools, visualise variants using a genome browser, and annotate SNPs for predicted biological effects.

Recommended Participants

Biologists and other life scientists planning to work with next-generation sequencing data for small variant detection. 

Learning Objectives

  • Perform QC evaluation and filtering on next-generation sequencing data
  • Select and use relevant variant detection software and apply appropriate quality filters to screen variants
  • View variant and sequence data using the Integrative Genomics Viewer (IGV)
  • Carry out preliminary functional annotation of predicted variants

Syllabus

  • Access and use of the Galaxy bioinformatics analysis platform
  • Quality control and filtering of next-generation sequencing data
  • Next-generation sequencing read mapping
  • Visualisation of mapped reads with the Integrative Genomics Viewer
  • Use of and comparison of software applications to call genomic variants
  • Filtering and screening protocols to generate lists of high-confidence SNPs
  • Initial annotation of the predicted biological impact of identified variants

About Bioinformatics and genomics

If your research study involves bioinformatics and genomics, we've got you covered! The Graduate School works with different providers to provide a range of sessions with esteemed providers such as QCIF.

Useful links

  • Queensland Facility for Advanced Bioinformatics (QFAB): Bioinformatics, biostatistics and biodata expertise
  • Hacky Hour (supported by RCC, QCIF, IMB and wonderful volunteer helpers!): RCC runs consultations every Tuesday at Cafe Nano. Come and ask IT questions such as: getting started with Python and R, stats, machine learning, bio-image, software tools, research data management (RDM), how to access high performance computing, cloud data storage and tools for data cleaning and data visualisation. Bring your project's IT problems or come along as a helper! Very occasionally Hacky Hour may not run; follow us on Twitter (@HackyHourStLuc​) to get the latest announcements. Aside from the usual IT research questions, 
    • First Tuesday of the monthBioinformatics Hacky Hour, ask bioinformatics analysis, software and pipeline questions
    • Last Tuesday of the monthBioLab Hacky Hour, ask about experimental design and technical sample processing questions to get started in the lab