This tutorial was part of training workshop, RNA-seq Bioinformatics–Introduction to bioinformatics for RNA sequence analysis, hosted by Dr. Griffit, Professor of Medicine (Oncology) and Genetics and Assistant Director of the McDonnell Genome Institute at Washington University. It is well explained to how to use EC2 for bioinformatics.
Here are tutorials for the online cloud genomics workshop held by Dr. Swaine Chen et al. from the Genome Institute of Singapore. This workshop aimed at helping bioinformaticians transition to running workloads on AWS by providing step-by-step details, with a focus on EC2 and S3. This is the best one to start with to learn AWS for bioinformatics.
I ⁃ GIS x AWS Training
Overview
II ⁃ Start a virtual Linux
machine
III ⁃ Start a Linux machine from a shared
AMI
IV ⁃ Attach additional
storage
V ⁃ AWS
CLI
VI ⁃ Download data shared using Amazon
S3
VII ⁃ Run a basic
analysis
VIII ⁃ Create an image of EC2
instance
IX ⁃ Terminate EC2 instance & Save Volume
snapshot
X ⁃ Set up Linux machine from earlier created
AMI
XI ⁃ Create Volume from Snapshot and attach to
EC2
XII ⁃ Create S3 bucket, transfer and make objects
public
XIII ⁃ Share an AMI and an EBS snapshot with your
Collaborators
XIV ⁃ Exploring Billing and
Costs
XV ⁃ Cleaning
up
XVI ⁃ Appendix
This GitHub repo hosts a free and open source course “AWS for Bioinformatics”. Course Materials include this repo and a YouTube playlist. This is a more advanced and comprehensive course presented by Lynn Langit. Very good reference.
Here is a detailed tutorial showing how to use AWS HealthOmics for variant analysis. This tutorial was part of AWS workshop.
By completing this activity, you will be able to:
• Articulate the value proposition of AWS HealthOmics
• Load sequencing data into HealthOmics Storage
• Run a genomics secondary analysis workflow through HealthOmics
Workflows
• Load VCFs (variant data) into the Variant store and load variant
annotations into the Annotation store
• Query both variants and annotations through Athena
The content of this workshop is presented for self-paced or instructor led consumption. Attendees should expect a minimum of 1hr to complete core activities. For a more in-depth dive, 2hrs is recommended.
Best experience: AWS Hosted Event An AWS hosted event provides the best experience for completing this workshop. Contact your AWS account representative if you are interested in participating in the next available session.
Region availability Currently, events for this workshop can only be provisioned in AWS regions where AWS HealthOmics is available
This workshop is for IT administrators, bioinformaticians, and software developers who are interested in a managed experience for their genomics needs.
Some experience with AWS, omics data types, and bioinformatics data analysis is expected but not a strict requirement.
This workshop makes use of some CLI commands and coding in Python and SQL.
This workshop is designed for use at a hosted AWS event where managed AWS accounts are provided to attendees. As such attendees should not expect to incur any costs for resources created by this workshop.
Customers running this workshop outside of an AWS hosted event with their personal AWS accounts as a self-paced activity can expect a total cost of around 1-2 USD if completed within 2hrs.
Here is a detailed tutorial showing how to migrte nf-core workflows to AWS HealthOmics. This tutorial was part of AWS workshop.
By completing this activity, you will be able to:
• Understand how to migrate nf-core workflows into AWS HealthOmics
• Run a secondary analysis workflow through AWS HealthOmics Workflows
• Run and monitor a workflow with test data
This workshop can be part of an AWS instructor-led event. Attendees should expect a minimum of 1hr to complete core activities. For a more in-depth dive, 2hrs is recommended.
This workshop is for bioinformaticians and software developers who are interested in migrating an nf-core nextflow workflow to AWS HealthOmics - a purpose-built service that helps healthcare and life science organizations and their software partners store, query, and analyze genomic, transcriptomic, and other omics data and then generate insights from that data to improve health. It supports large-scale analysis and collaborative research.
Some experience with AWS and genomics is expected but not a strict requirement. Familiarity running ‘Nextflow’
This workshop is designed for use at a hosted AWS event where managed AWS accounts are provided to attendees. As such attendees should not expect to incur any costs for resources created by this workshop.
Customers running this workshop outside of an AWS hosted event with their personal AWS accounts can expect a total cost of around 1-2 USD if completed within 2hrs.
• Episode 2, following a detailed step-by-step guide with screenshots along the way is offered by the State Public Health BioInformatics Group. Setting Up Nextflow and AWS Batch