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.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

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

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:

AvatarSimon Gladman AvatarAnton Nekrutenko AvatarDelphine Lariviere AvatarCristóbal 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:

AvatarSimon Gladman AvatarAnna Syme AvatarHelena Rasche AvatarSaskia Hiltemann AvatarAnthony Bretaudeau AvatarAnton Nekrutenko AvatarDelphine Lariviere AvatarBazante Sanders AvatarMiaomiao Zhou AvatarAlexandre Cormier AvatarErwan Corre AvatarLaura Leroi AvatarStéphanie Robin AvatarWolfgang Maier AvatarAlex Ostrovsky AvatarCristóbal Gallardo