• NCGR NISE Bioinformatics
  • License and Copyright
  • 1 Instructors
  • 2 Getting Started
    • 2.1 Computer requirements
    • 2.2 Connecting to the linux server
  • 3 Linux
    • 3.1 A little shell… aka the $ prompt is the command line interface
    • 3.2 Directory Structure
    • 3.3 Find the shell in system you’ll use to log into the NCGR’s server
    • 3.4 Log on to logrus server
    • 3.5 Now that I logged on, where am I?
    • 3.6 Part I: Basic Topics
      • 3.6.1 Understanding Directories
      • 3.6.2 Listing options
      • 3.6.3 Navigation
      • 3.6.4 Files: creating with touch command
      • 3.6.5 History command
      • 3.6.6 Files: creating by redirecting standard out
      • 3.6.7 File name completion with tab
      • 3.6.8 Files: moving files from one filename to another
      • 3.6.9 Files: copying files from one filename to another
      • 3.6.10 Files: securely copying files between your laptop and logrus
      • 3.6.11 Files and directories: removing files is deleting files
      • 3.6.12 Tool box: How to abort a command/process
    • 3.7 PART II: Advanced Topics
      • 3.7.1 Files: Symbolic links and the soft link (-s)
      • 3.7.2 Understanding a fasta file format
      • 3.7.3 Understanding fastq (fq) file format
      • 3.7.4 Using grep (global regular expression print) to extract metrics
      • 3.7.5 Working with compressed files
      • 3.7.6 Start ^ and end $ symbols
      • 3.7.7 Files: parsing and creating data-subsets
      • 3.7.8 Files: parsing and creating data-subsets
      • 3.7.9 Files: parsing and creating data-subsets
      • 3.7.10 Files: parsing and creating data-subsets
      • 3.7.11 Revisiting table1 and previous awk command
      • 3.7.12 Files: Stream EDitor (sed)
      • 3.7.13 The Bash “for” Loop
      • 3.7.14 Help with command syntax
    • 3.8 Exercises
    • 3.9 PART III
    • 3.10 More Exercises
    • 3.11 Jeopardy
  • 4 Our World in Data (parsing)
    • 4.1 Practice parsing
    • 4.2 Our World in Data
    • 4.3 Practice with your 3 countries
    • 4.4 Country files
    • 4.5 Jeopardy
  • 5 NCBI SARS-CoV-2 Genome Sequences
    • 5.1 Getting Sequences from NCBI
    • 5.2 Exploring Sequence Files
    • 5.3 Practice with your 3 countries
    • 5.4 Plotting
    • 5.5 R
    • 5.6 ggplot2
      • 5.6.1 Histogram of Collection Dates
      • 5.6.2 Plot Length x Variants
      • 5.6.3 BONUS
      • 5.6.4 Plot Collection Date x Variants
      • 5.6.5 Plot Collection Date x Variants for your 3 countries
  • 6 Our World in Data (plots)
    • 6.1 Bar chart
    • 6.2 Line chart
    • 6.3 Plot all 3 countries + transparency
  • 7 GISAID SARS-CoV-2 Genome Sequences
    • 7.1 GISAID
    • 7.2 Phylodynamics
    • 7.3 Genome sequences
    • 7.4 Upload sequences
  • 8 Multiple Sequence Alignment
    • 8.1 SARS-Cov-2 variant genomes
    • 8.2 Spike protein
    • 8.3 Arcturus Genomes
    • 8.4 Omicron Recombinant Case study
  • 9 Phylogenetic Trees
    • 9.1 SARS-Cov-2 variant genomes
    • 9.2 Visualizing the tree
    • 9.3 Arcturus Genome Sequences
    • 9.4 Spike Protein
    • 9.5 Spike Protein
  • 10 Dotplots
    • 10.1 SARS-CoV-2
    • 10.2 Yersinia
  • 11 Ancient Pandemic
  • 12 Wastewater
    • 12.1 Wastewater data
    • 12.2 Map of wastewater sites
    • 12.3 Read alignments
    • 12.4 Identify SARS-CoV-2 variants
    • 12.5 SARS-CoV-2 variant piecharts
  • 13 Wrap Up
    • 13.1 Acknowledgements
    • 13.2 Survey
    • 13.3 Questions
    • 13.4 Server access and acknowledgements
    • 13.5 Bookdown document
    • 13.6 Zoom recordings
  • © National Center for Genome Resources
  • Published with bookdown

NCGR NISE-Bioinformatics

NCGR NISE-Bioinformatics

License and Copyright

License: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 https://creativecommons.org/licenses/by-nc-nd/4.0/

© 2023-2024 National Center for Genome Resources


This publication was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103451.