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 Recordings Input dataset Workflows Galaxy servers
An Introduction to Genome Assembly
plain text tutorial
  • An introduction to get started in genome assembly and annotation
    plain text
    Assembly of metagenomic sequencing data 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 Quality Control plain text 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
  • VGP assembly pipeline tutorial
    VGP assembly pipeline - short version 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:

    orcid logoAvatarSimon GladmanAvatarAnton NekrutenkoAvatarDelphine LariviereAvatarCristóbal 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:

    orcid logoAvatarSimon GladmanAvatarAnna Symeorcid logoAvatarHelena Rascheorcid logoAvatarSaskia Hiltemannorcid logoAvatarAnthony BretaudeauAvatarAnton NekrutenkoAvatarDelphine Lariviereorcid logoAvatarAlexandre Cormierorcid logoAvatarErwan Correorcid logoAvatarLaura Leroiorcid logoAvatarStéphanie RobinAvatarErasmus+ ProgrammeAvatarWolfgang MaierAvatarAlex OstrovskyAvatarCristóbal GallardoAvatarLinelle AbuegAvatarBrandon PickettAvatarGiulio FormentiAvatarMarcella Sozzoni