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Long-read de novo assemblies

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Setup for the workshop

Overview

Teaching: 10 min
Exercises: 10 min
Questions

  • Installation of the VirtualBox image

Objectives

  • To have the Ubuntu VM running in VirtualBox, or

  • To know which tools to used and where to find the data for local installation

For the workshop we use Ubuntu Linux as the main Operating System. We have created a VirtualBox image, including all the necessary tools and data. You are of course welcome to use your own Linux-based system.

Installing the VirtualBox image

VirtualBox is a virtualization tool from VMWare and is freely available.

Please download the The Ubuntu image and store it on a local hard drive. A network location usually does not work, so it is better to store it locally.

The next steps will install and run the Ubuntu image:

  1. Start VirtualBox
  2. Select New from the top-left (the blue ‘star’)
  3. Give the virtual machine a name, for example Genomics. Type is Linux and Version Ubuntu (64-bit), or Linux (64-bit). Click ‘next’.
  4. Select Memory size: keep the setting in the green, but above 1GB. For this workshop we recommend to use 80% of the available memory. Click ‘next’
  5. Load the image by selecting ‘Use an existing virtual hard disk file’ and locate the .vdi file. Click ‘create’.
  6. Open Settings -> System -> Processor and select almost all CPUs: leave 1 for the host.
  7. Clicking Start (green arrow) should now start Ubuntu and you will automatically login.
  8. It is now recommended to leave the host system alone and work only on the Ubuntu virtual machine.

The image is a regular Ubuntu install, so if you install this on your laptop or desktop you can continue to use it.

The password for the user is genetwister and the Ubuntu user has superuser access (‘sudo’).

Installing the data and tools on your own Ubuntu

The list of tools used for workshop:

  1. Java 8
  2. Assembly-stats
  3. Minimap2
  4. Canu
  5. Platanus
  6. Mummer 4
  7. Samtools & BCF tools
  8. Tablet
  9. Integrative Genomics Viewer (optional)

The workshop code folder contains a shell-script installing_workshop_vm.sh which installs all required packages.

The data are available from Dropbox.

Origin of the data

For this workshop we have selected read data sets and a particular region of a cultivar of Arabidopsis thaliana (Thale cress).

Rounding up

The data folders also contains, next to the raw data, all intermediate and end results. So if for some reason a step in the exercise fails to produce any results you can still continue.

Key Points

  • VM can be used after the workshop

  • Installing required packages on own machine may require root privileges.

Used applications

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