UNIX and NGS
praha-november-2021
  • Installation instructions
  • Connecting to the remote machine
  • Session 1: Basic Unix
  • Session 2: Genomic data
  • Session 3: Plain text file processing in Unix
  • Session 4: Unix - “Real” Project
  • Session 5: Graphics session
  • Session 6: Read quality
  • Session 7: Genome assembly
  • Session 8: Bioinformatic pipelines
  • Session 9: Variant quality
  • Links
    • Advanced Bash
    • Bash command help re-imagined
    • Some fun
    • R Studio
    • Visual design
    • Genomic tools
    • Genomic data formats
  • A few more tips
  • Reference manual for Unix introduction
  • Important NGS formats
  • Additional exercises
  • Course materials preparation
  • Slide decks
UNIX and NGS
  • Docs »
  • Links
  • Edit on GitHub

Links¶

Here is few sources that you can go through, when you get bored during the course…

Advanced Bash¶

  • Advanced Bash-Scripting Guide
  • Bash one-liners explained
  • How redirection really works
  • What version of bash you need for X to work
  • The Bash Primer
  • Explanation of a scrollback buffer

Bash command help re-imagined¶

  • tldr pages
  • explainshell

Some fun¶

  • Bash game to celebrate 50th anniversary
  • Regex golf
  • Regex test and explain
  • Faces behind Unix

R Studio¶

  • A few nice cheat sheets

Visual design¶

  • Martin Krzywinski: Keynote on Visual Design Principles
  • Nature Methods’ Points of View
  • Gestalt principles 1
  • Gestalt principles 2
  • Well designed color palettes

Genomic tools¶

  • Bedtools
  • Vcftools

Genomic data formats¶

  • VCF
  • GFF
  • BED
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