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
• slides Slides: Quality Control
• tutorial Hands-on: Quality Control

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

Contributors

This material was contributed to by:

Cristóbal Gallardo

Bérénice Batut

Saskia Hiltemann

Polina Polunina

Laura Leroi

Giulio Formenti

Linelle Abueg

Anthony Bretaudeau

Miaomiao Zhou

Bazante Sanders

Tom Brown

Avans Hogeschool

Anna Syme

Alexandre Cormier

Marcella Sozzoni

Erwan Corre

Brandon Pickett

Fabian Recktenwald

Alex Ostrovsky

Helena Rasche

Wolfgang Maier

Anton Nekrutenko

Simon Gladman

Delphine Lariviere

Stéphanie Robin

Funding

These individuals or organisations provided funding support for the development of this resource

ABRomics

Gallantries

This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.