TL;DR


Why call it ‘fastQsee’ though 🤔?

Well, because you will get to see 👀 a FastQC report of your FASTQ file very fast! Installation-less and quick, made possible by a little container magic from Docker and powered by Deploit.


What will I learn?

This tutorial is a primer, on how to go modular and use Docker 🐳 containers for your bioinformatics analysis tasks. More specifically, we will learn how to use the Deploit platform to assemble and deploy on cloud a reproducible and sharable bioinformatics workflow.

We will assemble the following resources into a workflow on the Deploit platform:

  • 🐳 a Docker container, from DockerHub
  • 🚀 a curated pipeline, available on the Deploit platform
  • 📜 a 1000genomes project fastq.gz file, fetched from an EMBL-EBI FTP site


Last things first: What results will I get from the FastQC tool on Deploit?

After completing this mini workflow on the Deploit platform, you will have:
1) a plot-full FastQC html report,
with key metrics to assess the quality of your FASTQ file

2) sharable links to your Job Page s ,
with interactive plots and information about the resources and the results.

You can access the Jobs Pages from the sharable urls we created for this example:

  • for retrieving the 1000genomes fastq.gz file : 🔗 wgetGunzipper
  • for generating the FastQC html report: 🔗 fastQsee

and take a look at what a Job Page looks like below: