Assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Requirements
Before diving into this topic, we recommend you to have a look at:
- Introduction to Galaxy Analyses
-
Sequence analysis
- Quality Control: slides slides - tutorial hands-on
Material
Lesson | Slides | Hands-on | Input dataset | Workflows | Galaxy tour |
---|---|---|---|---|---|
De Bruijn Graph Assembly
|
slides | tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour |
Introduction to Genome Assembly
|
slides | tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour |
Making sense of a newly assembled genome
prokaryote
|
tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour | |
Unicycler Assembly
level level level
prokaryote
|
slides | tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour |
Galaxy instances
You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
You can also use the following Docker image for these tutorials:
docker run -p 8080:80 quay.io/galaxy/assembly-training
NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.
It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password admin to access everything.
Maintainers
This material is maintained by:
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
Contributors
This material was contributed to by: