Introduction to Linux for bioinformatics

Linux is a very popular operating system in bioinformatics. In this training you will learn why that is and how it can help you with your bioinformatics analysis. After this training you will be able to:

• install software on Linux
• use command line to run tools
• use command line to handle files
• write small scripts to automate your analysis

Training material

• slides day 1
• slides day 2

Additional information

• Linux Beginner's Cheat page
• The practical command line cheat sheet
• AWK
• Terminal keyboard shortcuts
  
  

Exercises during the training

Excercises: Part 1

On the training there is a Linux Ubuntu installation available on a Google cloud environment. To access Linux we use Google Chrome and the 'VNC Viewer for Google Chrome' application.
When you launch the application, you have to enter an IP address, this will be mentioned on the training.

Installing Linux

• Create a bootable live USB drive for testing distributions
• Create a virtual machine running a Linux distribution using VirtualBox

Installing software

Install the tools from the presentation slides. Note that when you install something, everyone in the training has access to that tool!
Here are some exercises to try on your personal Linux installation:

• Install Geany, a powerful, light-weight programming editor
• Adding a new software repository for bioinformatics
• Example of downloading and installing an .deb file
• Download and install the Kent tools, a collection of binaries and scripts
• optional Adding repositories containing bioinformatics tools in Red Hat-derived distributions
• optional Useful bioinformatics software packages in Linux
• Additional Bioinformatics repositories

Command line

• Gentle introduction to the command line
• Downloading and storing bioinformatics data

File system

• Compression and archiving
• Symbolic links

Bonus

• Installing and compiling examples

Excercises: Part 2

Text mining, scripting and 'for' loops

• Simple bash script
• Download a simple perl script
• Text analysis on the command line
• Bash aliases to enhance your productivity
• Writing for loops

NGS intro

• Linux command line#installing cutadapt
• Linux command line#Quality control of NGS data

Bonus

• Install Picard tools in Linux
• Combine the content of several fastq files into one big fastq file

EXTRA

Bioinformatics oneliners

Sneak preview to duplication rate of reads

gunzip -dc fastq.gz | head -n 1000000 | awk '{ if(NR%4==2) { print $1 } }' | sort | uniq -c | sort -g > sorted_duplicated

Convert fastq to fasta

paste - - - - < in.fq | cut -f 1,2 | sed 's/^@/>/' | tr "\t" "\n" > out.fa

Count all the variants called in all the vcf files

cat *.vcf | grep -v '^#' | wc -l

Count all the variants in three vcf files

cat *.raw.vcf | grep -v '^#' | awk '{print $1 "\t" $2 "\t" $5}' | sort | uniq -c | grep ' 3 ' | wc -l

Software installation exercises

• Adding the Debian Med repository containing bioinformatics tools in Debian-derived distributions