Coverage analysis from the command line

Concepts and simple tools to evaluate the sequence coverage…

Pigz: a faster alternative to gzip for big files

Using multiple threads to compress files but maintaining compatibility with gunzip

The gzip program is incredibly popular among Linux applications, in spite of some…

Is a Bash variable set?

Preventing unbound variables is good, but we need a way to tell if a variable has no content or has never been initialized

Merging Illumina lanes with a Bash script

This article describes a Bash script to perform a simple task with some controls and best practices.

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…

A simple introduction to XML and JSON

Two popular formats to store structured data, that are also…

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…