UNIX and NGS
praha-january-2016
  • 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
    • 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...

Bash¶

  • http://www.tldp.org/LDP/abs/html/
  • http://www.catonmat.net/blog/bash-one-liners-explained-part-three/
  • http://wiki.bash-hackers.org/howto/redirection_tutorial
  • http://wiki.bash-hackers.org/scripting/bashchanges

R Studio¶

  • http://www.rstudio.com/resources/cheatsheets/

Visual design¶

  • one secret link you got by email
  • http://www.smashingmagazine.com/2014/03/28/design-principles-visual-perception-and-the-principles-of-gestalt/
  • http://www.vanseodesign.com/web-design/gestalt-principles-of-perception/
  • http://colorbrewer2.org

Genomic tools¶

  • http://bedtools.readthedocs.org/en/
  • http://bedops.readthedocs.org/en/
  • http://vcftools.sourceforge.net

Genomic data formats¶

  • http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40
  • http://www.ensembl.org/info/website/upload/gff.html
  • https://genome.ucsc.edu/FAQ/FAQformat.html#format1
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