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.
|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|
|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|
|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|
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.
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).