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 FR JA ES PT AR	zenodo_link	workflow	interactive_tour
Introduction to Genome Assembly	slides	tutorial Toggle Dropdown FR JA ES PT AR	zenodo_link	workflow	interactive_tour
Making sense of a newly assembled genome prokaryote		tutorial Toggle Dropdown FR JA ES PT AR	zenodo_link	workflow	interactive_tour
Unicycler Assembly level level level prokaryote	slides	tutorial Toggle Dropdown FR JA ES PT AR	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:

Simon Gladman,

Anton Nekrutenko,

Delphine Lariviere

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:

Delphine Lariviere