Coverage analysis from the command line

Concepts and simple tools to evaluate the sequence coverage…

Downloading NGS data sets from the command line

Short reads data sets can be automatically downloaded from the Linux terminal

Sequencing data archives

A small introduction to Bash scripting (Part 1)

Bash scripting basics for biologists turning…

Testing regular expressions in a Bash script

I noticed that several shell script would be simpler and more powerful if they adopted some pattern matching, but this technique so widely adopted in most scripting languages (like Python, PHP and — of course — Perl) is less used in Bash scripts.

For loops (Bash scripting, Part 2)

A bioinformatic example of a for loop

After a small introduction to Bash scripting, we finally create a first bioinformatics script… introducing one of the loops we can use with the shell. A loop is a structure that…

If, then. Condition checking for Bash scripts (Part 3)

The idea to check if some condition is true before executing some commands is very simple and useful. The Bash syntax, for historical reasons, is probably the ugliest you’ll ever see but after a while it will stop scaring you (and your…

Bash scripting safety net (Part 4)

Best practice to avoid common errors in Bash scripts, preventing execution if errors occur: “set -euo pipefail”

Bash script getting parameters from the users (Part 5)

An introduction to arguments passed from the user to our shell scripts.

A basic introduction on passing parameters to shell scripts