Welcome to the BPA-CSIRO workshops project on GitHub. This serves as a landing page for the various training workshops organised and maintained by BPA-CSIRO. An overview of the training workshops and included training modules are described below. For the latest upcoming BPA-CSIRO workshops, please visit the Bioplatforms Australia training page.
Cancer Genomics
The Cancer Genomics workshop aims to provide an introduction to cancer genomics analytical pipelines for single nucleotide variations (SNV), copy number variations (CNV) and structural variations (SV).
| Training Modules |
|---|
| Introduction to Command Line |
| Data Quality |
| Read Alignment |
| Single Nucleotide Variant Calling and Annotation |
| Copy Number Variation |
| Structural Variant Analysisy |
| Variant Visualisation |
Introduction to Next Generation Sequencing Hands-on Workshop
This is a practical 3 day hands-on course designed for bench biologists, PhD students or early career postdoctoral researchers with no or basic bioinformatics experience who are planning or currently using NGS approaches in their research area. It will include a half-day introduction to the command line interface. The training modules included in this workshop are listed below:
| Training Modules |
|---|
| Introduction to Command Line |
| Data Quality |
| Read Alignment |
| ChIP-Seq |
| RNA-Seq |
| de novo Genome Assembly |
Getting Started
The Introduction to Next Generation Sequencing Hands-on Workshop image can be
launched on the NeCTAR Research Cloud and Amazon Web Services (AWS) cloud platforms.
A detailed guide on launching the image on the NeCTAR Research Cloud
is available here.
The latest virtual machine on the NeCTAR Research Cloud is:
| Name | ID |
|---|---|
BTP-2016-01-25 |
9c7fd8ac-5cfe-4067-aae3-82e53a49def3 |
A detailed guide for launching the image on AWS is also available here. On AWS, the latest virtual machine image (AMI) is available on the following regions:
| Region | AMI |
|---|---|
ap-southeast-2 |
ami-be597ddd |
eu-west-1 |
ami-d3a31ea0 |
Stand-alone virtual machine images are also available for VirtualBox and VMWare. These are downloadable from here. Once downloaded, it can be loaded straight into VirtualBox or VMWare. VirtualBox or VMWare must be installed on the client machine.
The latest handouts for the Introduction to Next Generation Sequencing Hands-on Workshop
are available here.
Licence
All of these components, scripts and configuration tools make up the BTP and are managed and available on GitHub (https://github.com/BPA-CSIRO-Workshops) and are licensed under a Creative Commons Attribution 3.0 Unported License.