UNIX and NGS
praha-february-2019
  • Installation instructions
  • Connecting to the virtual machine
  • Unix - Basics
  • Unix - Advanced I
  • Unix - Advanced II
  • Graphics session
  • Read quality
  • Genome assembly
  • Genomic tools session
  • Variant quality
  • Links
    • Advanced Bash
    • R Studio
    • Visual design
    • Genomic tools
    • Genomic data formats
  • Best practice
  • 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

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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