RADseq cloud tutorial

This step-by-step tutorial is a risk-free paragliding tandem flight into the cloud. We will guide you through the process of leveraging the cloud to analyse your RADseq data.

For an evolutionary biologist, restriction site-associated DNA sequencing (RADseq) and new genomic tools are great opportunities, but the fast-changing field can be very challenging to follow. The most important tool for RADseq, after your brain and the sequencer, is your computer. RADseq analysis can be very demanding on personal computers, there can be not enough CPU and/or memory and the analysis can crash or worse, your computer is now solely dedicated to this task and nothing else. If you’re lucky enough to have access to a large up-to-date university computer clusters this might be a good solution but they come with their share of problems.

We chose Amazon Elastic Compute Cloud (EC2) because: (i) it’s relatively easy, their’s extensive documentation and big community to ask for help; (ii) it’s relatively cheap to use machines with lots of CPU and memory. Using the cloud offers 2 more advantages:

1. you can write off computer and software cost as an operating expense rather than a capital or service expenditure (depending on countries and universities).
2. you control everything: no need to ask IT to update one of the numerous dependenices you’ll likely required…

Assumptions

Although you can go through this tutorial with copy and paste commands, knowing very basic Terminal commands will be useful:

• Reference card: quite useful to get through the jargon and main commands.
• Good reading: to understand the basic steps to install software with the terminal.
• Online courses: e.g. with DataCamp.

Recommendations:

In the beginning most students will feel lost and very intimidated by everything related to computers, software and RADseq analysis. Commonly the end result is that your scientific work flow is impeded. If you’re at the Master and PhD level and all the RADseq stuff is overwhelming and you’re not sleeping at night, consider:

• you should focus first on biology, second, on bioinformatics (a computer is the main tool you’ll likely use in your future) and if you have time, the wet-lab part. Now, don’t get me wrong, I think the wet-lab is the most important step, but unless you want to become a wet-lab technician, my advice is stay away as much as humanly possible from the wet-lab and leave it to experts.

• asking for help:

  • ask your director to be supervised by a PostDoc who knows the ropes in exchange for authorship on the paper(s).
  • ask for outside help, there’s a lot of sequencing facilities that now offers to do the extractions, librairies, sequencing and genotyping.

Thierry Gosselin