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Welcome to the Introduction to NGS Workshop


The Introduction to NGS Data Analysis is a Two-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 QC, Alignment, RNA-Seq data and de novo genome assembly.

Time Table

Time Subject notes
Day1: 22 June 2020
10:00-10:20 am Housekeeping + Icebreaker Slides + group activity
10:20:10-30 pm short Break
10:30-11:40 am Intro to command line Interactive Lecture
11:45:12:45 pm Intro to R Live coding
12:45-1:45 pm Lunch Break
1:45-2:45 pm QC of NGS data Hands-on
2:45-3:00 pm Recap + QA Group discussion
Time Subject notes
Day 2: 24 June 2020
10:00-10:15 am Workflow activity group activity
10:15-10:30 am NGS alignment Practice
10:30-11:30 am RNAseq alignment exploration in IGV Practice
11:30-11:40 pm short Break
11:40-12:00 pm Transcript assembly exploration in IGV Practice
12:00 -1:00 pm RNAseq: DE using edgeR Practice
1:00-2:00 pm Lunch Break
2:00 - 2:30 pm RNAseq: DE using edgeR Practice
2:30-3:00 pm QA and Wrap up
Time Subject notes
Day3: 25 June 2020
10:00-10:15 am Intro to denovo assembly Lecture Recap
10:15-11:15 am Compile and explore Velvet + read data Practice
11:15-11:30 am Assembly activity I group activity
11:30-12:00 pm Perform short read assembly using different settings Practice
12:00-1:00 pm Lunch Break
1:00-1:30 pm Assembly results discussion
1:30-2:00 pm Assembly visualization and exploration Practice
2:00-3:00 pm Long read assembly

Workshop Content

Topics covered by this workshop include:

  • An introduction to R programming

  • An Introduction to the command line interface and NGS file formats

  • Quality control of sequencing data

  • NGS read alignment

  • Basic RNA-Seq differential expression analysis

  • Short and long read de novo genome assembly

This workshop will be delivered using a mixture of lectures, hands-on practical sessions, and open discussions.

Acknowledgements

This workshop was developed by Bioplatforms Australia, in partnership with CSIRO, and with support from the European Bioinformatics Institute (EBI), a member of the European Molecular Biology Laboratory (EMBL) in the UK. The workshop content has been maintained and updated by a network of dedicated [bioinformatics trainers] (http://www.bioplatforms.com/bioinformatics-training/) from around Australia.

The Bioinformatics Training Platform was developed in collaboration with the Cloud team of Monash eResearch Platform and this workshop has been hosted on Nectar infrastructure.

This workshop is possible thanks to funding support from the Commonwealth Government National Collaborative Research Infrastructure Strategy (NCRIS).