Fundamentals in NGS Data Analysis

Fundamentals in NGS Data Analysis is a three-day, hands-on workshop that offers attendees a basic understanding of NGS data analysis workflows. The workshop provides hands-on computational experience in analysis of NGS data using common analytical approaches for ChIP-Seq, RNA-Seq data and de novo genome assembly.

Workshop Outline

Topics covered by this workshop include:

  • An introduction to the command line interface and NGS file formats
  • Assessment of the quality of NGS sequence reads
  • Sequence alignment algorithms
  • Basic ChIP-Seq analysis
  • Basic RNA-Seq analysis
  • de novo genome assembly

Workshop Dates

City Location Date Workshop Costs
Perth Curtin University 12th July – 14th July 2016 $495 (Plus GST)

Recommended Participants

Fundamentals in NGS Data Analysis workshop is designed for bench scientists, PhD students and early career postdoctoral researchers who require NGS in their research area but have minimal bioinformatics experience. The workshop utilises the Linux command-line, although no prior programming experience is required.

Workshop Co-ordinators

Katherine Champ, Bioplatforms Australia (kchamp@bioplatforms.com)

Draft Program

Day 1 – Introduction to the command line, data quality & alignment & ChIP-Seq

Time

Topic

09:00 – 09:45 Introductions and course orientation
09:45 – 10:15 Practical: Introduction to the command line
10:15 – 10:40 Morning Tea
10:40 – 11:20 Practical: Introduction to the command line (cont.)
11:20 – 11:45 Introduction to NGS Course
11:45 – 12:30 Introduction to NGS – Technology, data formats and quality control
12:30 – 13:15 Lunch
13:15 – 13:25 Quality control intro to practical
13:25 – 14:05 Practical: Quality Control
14:05 – 14.15 Introduction to sequence alignment
14:15 – 15:00 Practical: Sequence Alignment
15:00 – 15:25 Afternoon Tea
15:25 – 15:55 Introduction to ChIP-Seq
15:55 – 17:30 Practical: ChIP-Seq analysis – Peak calling and annotation

Day 2 – ChIP-Seq motif analysis and RNA-Seq analysis

Time

Topic

09:00 – 09:40 Practical: Motif analysis
09:30 – 10:30 Introduction to RNA-Seq
10:30 – 10:50 Morning Tea
10:50 – 12:30 Practical: Alignment and splice junction identification
12:30 – 13:30 Lunch
13:30 – 15:00 Practical: Transcriptome assembly
15:00 – 15:30 Afternoon Tea
15:30 – 17:30 Practical: Differential gene expression

Day 3 – Introduction to de novo genome assembly

Time

Topic

09:00 – 09:10 Welcome and introductions to Day 3
09:10 – 09:40 Introduction to de novo assembly
09:40 – 10:30 Practical: de novo assembly using velvet (single-end reads/pair-end reads)
10:30 – 10:50 Morning Tea
10:50 – 12:30 Practical: de novo assembly using velvet (single-end reads/pair-end reads)
12:30 – 13:30 Lunch
13:30 – 15:30 Practical: de novo assembly using velvet (hybrid assembly)
15:30 – 15:50 Afternoon Tea
15:50 – 16:30 Practical: de novo assembly using velvet (hybrid assembly)
16:30 – 17:50 Review and discussion of Velvet de novo assembly exercises

Registration and Payment

Workshop places are limited due to the significant practical component of this workshop. To manage the high demand, all workshop applicants are subject to a selection process and MUST complete the online application form to be considered for a place. Incomplete applications will not be considered. The application period closes 10th June 2016. Successful applicants will be notified no later than 15th June 2016. The workshop fee of $495.00 (plus GST) covers course material, computer access, lunch and refreshments. Payment can be made by cheque, EFT or credit card.

Contact

For further information contact Katherine Champ, kchamp@bioplatforms.com.

Training Updates

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Interested in Hosting a Bioinformatics Workshop?

If you are interested in hosting a bioinformatics workshop at your local organisation or institute please contact Katherine Champ on kchamp@bioplatforms.com.
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