• 1. Data Carpentry Genomics Workshop - George Washington University
• 2. Workshop Code of Conduct
  • 2.1. Need Help?
  • 2.2. The Quick Version
  • 2.3. The Less Quick Version
• 3. Accessing The Atmosphere Cloud
• 4. Login & Launch Instance
• 5. SSH Secure-Login
• 6. Instance Maintenance
  • 6.1. Atmosphere Dashboard
  • 6.2. Suspend Instance
  • 6.3. Delete Instance
• 7. Additional Features
  • 7.1. Did you know you can access a shell terminal and a web-desktop via your browser ???
• 8. Advanced Topics
  • 8.1. Atmosphere Advanced Topics
• 9. Introducing the Shell
  • 9.1. What is a shell and why should I care?
  • 9.2. Navigating your file system
  • 9.3. Summary
  • 9.4. Moving around the file system
  • 9.5. Examining the contents of other directories
  • 9.6. Solution
  • 9.7. Full vs. Relative Paths
• 10. Bash lesson 2
  • 10.1. Working with Files
  • 10.2. Command History
  • 10.3. Examining Files
  • 10.4. Details on the FASTQ format
  • 10.5. Creating, moving, copying, and removing
  • 10.6. Searching files
  • 10.7. Redirecting output
  • 10.8. File manipulation and more practice with pipes
  • 10.9. Exercise
  • 10.10. Solution
  • 10.11. Writing for loops
• 11. Working with Bioconda.
  • 11.1. What is bioconda?
  • 11.2. What problems does conda (and therefore bioconda) solve?
  • 11.3. Installing conda and enabling bioconda
  • 11.4. Using conda
  • 11.5. Using bioconda
  • 11.6. Rstudio - Getting started
• 12. Workflow_Overview
• 13. Bioinformatics workflows
• 14. Assessing Read Quality
• 15. Starting with Data
• 16. Quality Control
  • 16.1. Details on the FASTQ format
  • 16.2. Assessing Quality using FastQC
  • 16.3. Running FastQC
  • 16.4. Viewing the FastQC results
  • 16.5. Decoding the other FastQC outputs
• 17. Trimming and Filtering
• 18. Cleaning Reads
  • 18.1. Trimmomatic Options
  • 18.2. Running Trimmomatic
• 19. Variant Calling Workflow
• 20. Alignment to a reference genome
• 21. Setting up
  • 21.1. Index the reference genome
  • 21.2. Align reads to reference genome
  • 21.3. Sort BAM file by coordinates
  • 21.4. Variant calling
  • 21.5. Explore the VCF format:
  • 21.6. Assess the alignment (visualization) - optional step
  • 21.7. Other Notes
• 22. Automating a Variant Calling Workflow
  • 22.1. What is a shell script?
• 23. Analyzing Quality with FastQC
• 24. Automating the Rest of our Variant Calling Workflow
• 25. Snakemake Basic Tutorial
• 26. Open Rstudio
• 27. Getting started - your first Snakefile
  • 27.1. Updating the Snakefile to track inputs and outputs
  • 27.2. Forcibly re-running things
• 28. Multiple rules
• 29. A first refactoring: adding a better default rule
• 30. A second refactoring: doing a bit of templating
• 31. Refactoring 3: templating output files, too
  • 31.1. Adding some more files
  • 31.2. Rerunning snakemake
• 32. Building out the workflow
  • 32.1. Providing input files explicitly to the multiqc rule
  • 32.2. Refactoring this to make it slightly more concise –
  • 32.3. Digression: what files does snakemake check in order to decide about rerunning?
  • 32.4. Making a clean rule
  • 32.5. Digression: running things in parallel
  • 32.6. Doing more things in our workflow.
• 33. More advanced snakemake
  • 33.1. Dry run
  • 33.2. Running things in parallel, revisited
  • 33.3. Specifying software required for a rule
  • 33.4. Outputting the entire workflow diagram
  • 33.5. Snakemake Report
• 34. Final thoughts - writing your own snakefile
  • 34.1. Dealing with complexity
• 35. Thinking about workflows - a strong(er) argument
• 36. Go forth and Workflow!
• 37. Advanced Topics
• 38. Transferring Data to and from an Instance
  • 38.1. Transferring Data using iCommands
• 39. Creating custom Atmosphere Images
• 40. ssh-rsa-key for password-less login
• 41. Tmux & Screen
• 42. SSH Remote host ID Changed Error