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.You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.
Before diving into this topic, we recommend you to have a look at:
- Introduction to Galaxy Analyses
- Sequence analysis
An Introduction to Genome Assembly
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An introduction to get started in genome assembly and annotation
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|Chloroplast genome assembly||tutorial Toggle Dropdown||
De Bruijn Graph Assembly
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Deeper look into Genome Assembly algorithms
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|Genome Assembly of MRSA using Illumina MiSeq Data||tutorial Toggle Dropdown|
|Genome Assembly of MRSA using Oxford Nanopore MinION Data||tutorial Toggle Dropdown|
|Genome assembly using PacBio data||tutorial Toggle Dropdown|
|Making sense of a newly assembled genome||tutorial Toggle Dropdown|
|Unicycler Assembly||plain text Toggle Dropdown||tutorial Toggle Dropdown|
|Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads||plain text Toggle Dropdown||tutorial Toggle Dropdown||
|VGP assembly pipeline||tutorial Toggle Dropdown|
|VGP assembly pipeline - short version||tutorial Toggle Dropdown|
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 QuestionsCommon 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.
This material is maintained by:Simon Gladman Anton Nekrutenko Delphine Lariviere Cristóbal Gallardo
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
This material was contributed to by:Simon Gladman Anna Syme Helena Rasche Saskia Hiltemann Anthony Bretaudeau Anton Nekrutenko Delphine Lariviere Bazante Sanders Miaomiao Zhou Avans Hogeschool Alexandre Cormier Erwan Corre Laura Leroi Stéphanie Robin Erasmus+ Programme Wolfgang Maier Alex Ostrovsky Cristóbal Gallardo Linelle Abueg Brandon Pickett Giulio Formenti Marcella Sozzoni