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:

Bérénice Batut

Anton Nekrutenko

Anthony Bretaudeau

Cristóbal Gallardo

Delphine Lariviere

Fabian Recktenwald

Saskia Hiltemann

Erwan Corre

Linelle Abueg

Anna Syme

Giulio Formenti

Laura Leroi

Marcella Sozzoni

Polina Polunina

Avans Hogeschool

Alex Ostrovsky

Stéphanie Robin

Wolfgang Maier

Simon Gladman

Alexandre Cormier

Bazante Sanders

Brandon Pickett

Helena Rasche

Miaomiao Zhou

Funders

This material was funded by:

Gallantries

ABRomics