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

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.

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Editorial Board

This material is reviewed by our Editorial Board:

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.

Contributors

This material was contributed to by:

Giulio Formenti

Simon Gladman

Avans Hogeschool

Alex Ostrovsky

Anthony Bretaudeau

Wolfgang Maier

Helena Rasche

Erwan Corre

Anton Nekrutenko

Marcella Sozzoni

Saskia Hiltemann

Stéphanie Robin

Polina Polunina

Bérénice Batut

Linelle Abueg

Bazante Sanders

Alexandre Cormier

Laura Leroi

Miaomiao Zhou

Brandon Pickett

Cristóbal Gallardo

Anna Syme

Fabian Recktenwald

Delphine Lariviere

Funders

This material was funded by:

Gallantries

ABRomics