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:

Material

Lesson Slides Hands-on Input dataset Workflows Galaxy tour
An Introduction to Genome Assembly
level level level
slides tutorial zenodo_link workflow interactive_tour
Chloroplast genome assembly
tutorial zenodo_link workflow
De Bruijn Graph Assembly
level level level
slides tutorial zenodo_link workflow interactive_tour
Deeper look into Genome Assembly algorithms
level level level
slides
Genome Assembly of MRSA using Illumina MiSeq Data
tutorial zenodo_link workflow
Genome Assembly of MRSA using Oxford Nanopore MinION Data
tutorial zenodo_link workflow
Making sense of a newly assembled genome
tutorial zenodo_link workflow interactive_tour
Unicycler Assembly
level level level
slides tutorial zenodo_link workflow interactive_tour
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
level level level
slides tutorial zenodo_link workflow

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 password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Maintainers

This material is maintained by:

Simon GladmanSimon Gladman Anton NekrutenkoAnton Nekrutenko Delphine LariviereDelphine Lariviere Cristóbal GallardoCristóbal Gallardo

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:

Simon GladmanSimon Gladman Anna SymeAnna Syme Helena RascheHelena Rasche Saskia HiltemannSaskia Hiltemann Anthony BretaudeauAnthony Bretaudeau Anton NekrutenkoAnton Nekrutenko Delphine LariviereDelphine Lariviere Bazante SandersBazante Sanders Miaomiao ZhouMiaomiao Zhou Wolfgang MaierWolfgang Maier