Hello everyone. The purpose of this tutorial is to document our experience of using AWS and explore how we can use the plethora of AWS services for genomics research in Monash University Malaysia.
Earlier, we had a challenge in storage data and computational power to conduct a genome hybrid assembly. We approached AWS Singapore and was generously granted with a sum of POC credit. So while this tutorial touches on hard concepts of AWS, we will also see how we can use AWS services for bioinformatics analysis, assembly of eukaryotic genomes in particular.
- Notebook00. Activating Proof-of-Concept (POC) credits
- Notebook01. Starting an instance
- Notebook02-0. Set billing alarm
- Notebook02-1. Trying out Unicycler on our charged instance
- Notebook03-0. EC2 EBS Volume
- Notebook03-1. Checking EBS and continue Unicycling
- Notebook03-2. Unicycler is taking too long
- Notebook04-0. Easy spot pricing
- Notebook04-1. Setting up a new instance
- Notebook04-2. Hybrid assembly of E. Coli
- Notebook04-3. Assessing E. Coli genome assemblies
- Notebook05-0. Setting up Anaconda
- Notebook05-1. Jupyter Server
- Notebook05-2. RStudio Server
- Notebook06-0. Getting started with AWS S3
- Notebook06-1. Transferring files in S3
- Notebook06-2. Mounting S3 into EC2 instance
- IAM roles
- AWS S3
- Multiple instances
- Spot fleet
- AWS Batch
- Cromwell on AWS
- Falcon Genomics Pipelines