#!/ngs/sh

Downloading NGS datasets using Nextflow

A simple to use pipeline to download FASTQ files from NCBI or EBI, which serves as a good…

Manage shared software with environment “modules”

How to setup “module load” in your shared Linux…

Compressing FASTQ files for long term storage

The raw output of NGS experiments should be backed, and…

A simple introduction to XML and JSON

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

Merging Illumina lanes with a Bash script

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

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

A short introduction to Git and GitHub

The minimum workflow for keeping file revisions under control

When working on a script (or manuscript), version control enables the possibility to restore the last working version. Software…

Downloading NGS data sets from the command line

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

Sequencing data archives