Page Index - Green-Biome-Institute/AWS GitHub Wiki

130 page(s) in this GitHub Wiki:

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