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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