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 () and 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
    • An introduction to get started in genome assembly and annotation
    Assembly of metagenomic sequencing data
    assembly metagenomics
    Chloroplast genome assembly
    plants nanopore
    • De Bruijn Graph Assembly
    Deeper look into Genome Assembly algorithms
    Genome Assembly Quality Control
    assembly quality control
    Genome Assembly of MRSA using Illumina MiSeq Data
    illumina assembly amr
    Genome Assembly of MRSA using Oxford Nanopore MinION Data
    nanopore assembly amr
    Genome assembly using PacBio data
    assembly pacbio
    Large genome assembly and polishing
    assembly polishing nanopore
    Making sense of a newly assembled genome
    prokaryote
    Unicycler Assembly
    prokaryote
    Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
    covid19
    • VGP assembly pipeline
    pacbio eukaryote VGP
    VGP assembly pipeline - short version
    pacbio eukaryote VGP

    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 Nekrutenkoorcid logoAvatarDelphine Lariviereorcid logoAvatarCristóbal 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:

    AvatarMarcella Sozzoniorcid logoAvatarLaura Leroiorcid logoAvatarSaskia Hiltemannorcid logoAvatarErwan CorreAvatarAnton NekrutenkoAvatarLinelle Abuegorcid logoAvatarBérénice Batutorcid logoAvatarDelphine Lariviereorcid logoAvatarAnna SymeAvatarErasmus+ Programmeorcid logoAvatarAlexandre Cormierorcid logoAvatarSimon Gladmanorcid logoAvatarWolfgang Maierorcid logoAvatarHelena RascheAvatarAlex OstrovskyAvatarBazante Sandersorcid logoAvatarCristóbal Gallardoorcid logoAvatarAnthony Bretaudeauorcid logoAvatarStéphanie Robinorcid logoAvatarPolina PoluninaAvatarAvans HogeschoolAvatarBrandon PickettAvatarGiulio Formentiorcid logoAvatarMiaomiao Zhou