Page Index - Green-Biome-Institute/AWS GitHub Wiki
68 page(s) in this GitHub Wiki:
- Home
- Welcome to the AWS wiki!
- Here you will find information on the following:
- Tutorials / Trainings:
- Informational Content:
- Genome Assembly!
- Amazon Web Services Tutorials (For Scientists)!
- Analysis pipeline: From scratch to assembled genome on AWS
- Assembling with ABySS on EC2
- Assembling with Canu on EC2
- Assembling with Flye on EC2
- Assembling with MaSuRCA on EC2
- Assembling with NECAT on EC2
- Assembling with Raven on EC2
- Assembling with Shasta on EC2
- Assembling with SOAPdenovo2 on EC2
- Assembling with SparseAssembler on EC2
- Assembling with WENGAN on EC2
- Assembling with wtdbg2 on EC2
- Assembly QC with BUSCO
- Assembly QC with Quast
- Assembly Tutorial (Using a Chloroplast Genome)!
- Assembly with String Graph Assembler (SGA)
- AWS Elastic Cloud Computing (EC2) Instances
- AWS GBI AMI Documentation
- Billing, Cost Monitoring, and Budgets
- Checking to see what is in old AWS EBS Snapshots
- Chloroplast and Mitochondrial Assemblies from reads
- Command Vocabulary Sheet
- Data Storage with AWS S3
- Estimating what k mer parameter to use for a de bruijn graph based assembly (ABySS, Soapdenovo, Velvet)
- Filetypes and File Compression
- Finishing up after an assembly
- Genome Annotation Tools
- Identity and Account Management (IAM) users and logging into the Green Biome Institute AWS account
- Introduction to Amazon Web Services (AWS)
- Links to relevant softwares, papers, and resources
- Logging In and Navigating the AWS website
- Multiplexing terminals so that programs run in the background
- Recording time, cpu, and memory usage while running a program
- Resource Tags
- Section 1: Intro to Amazon Web Services, Identity & Access Management (IAM), and Billing
- Section 1: Introduction
- Section 2 Elastic Cloud Computing (EC2) and Elastic Block Store (EBS)
- Section 2: The Basics
- Section 3: Behind the Scenes
- Section 3: Simple Storage Service (S3) and the AWS CLI
- Section 4: Amazon Machine Images (AMI), the GBI AMI, and the GBI AWS Github as a Resource
- Section 4: Making, Moving, Copying, Editing, and Removing Files!
- Section 5 Starting our EC2 instance
- Section 5 : Setting up EC2 instance and Uploading Data
- Section 5: More complex but useful commands
- Section 6: Pre assembly software
- Section 6: Interacting with Other Computers & Virtual Terminal Sessions
- Section 7: Genome assembly with ABySS and SOAPdenovo2
- Section 7: Software Dependencies & More Complex Software Manuals
- Section 8: Checking our assembly quality and understanding our results
- Section 8: The Basics of Bash Scripting
- Section 9: Wrapping it All Up (All Review Questions)
- Sequencing Coverage necessary for de novo assembly
- SNS messages
- The Command Line Tutorial (For Scientists!)
- Trimming, Filtering, Genome Size Estimation
- Using "screen" to run jobs in the background
- Using the SRA toolkit for downloading SRA files
- What is the Command Line Interface? [Tutorial]
- What to do if your personal computer is not Linux?
- Wrapping it All Up (All Review Questions)