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Anna's hummingbird photo courtesy of VJAnderson{:.sc-intro-left}

Welcome to Galaxy for Genome Assembly

{:.no_toc}
The Genome Assembly Workbench is a comprehensive set of analysis tools and consolidated workflows to assist in Genome Assembly. The workbench is based on the Galaxy framework{:target="_blank"}, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.

Vertebrate Genomes Project


This workbench is also optimized to include all data, tools, and workflows associated with the __[Vertebrate Genomes Project (VGP)](https://vertebrategenomesproject.org/)__. All raw data published by the VGP is available from the remote data repository __Genome Ark__ in the data uploader. The VGP assembly workflows are available from the __Workflows__ tab within __Shared Data__. As new assemblies are generated, they will appear in __Histories__ in the __Shared Data__ tab.
# Content {:.no_toc}
  1. TOC {:toc}

Get started

Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take a [guided tour]({{ page.website }}/tours/core.galaxy_ui){:target="_blank"} through Galaxy's user interface.

VGP assembly training

We are working on a training with the objective of explaining how to execute the VGP genome assembly pipeline in Galaxy. You can find a draft in the Galaxy Training Network (GTN){:target="_blank"}.


Additional training material

All relevant materials for assembly-related data analysis can also be found within the GTN.

Lesson Slides Hands-on Input dataset Workflows Galaxy History
Welcome and introduction to Galaxy {:target="_blank"} / {:target="_blank"}
An Introduction to Genome Assembly {:target="_blank"}
A deeper look into Genome Assembly algorithms {:target="_blank"}
Quality Control {:target="_blank"} / {:target="_blank"} {:target="_blank"} / {:target="_blank"} {:target="_blank"} {:target="_blank"} []({{ page.website }}/u/gallardoalba/h/quality-control){:target="_blank"}
Mapping {:target="_blank"} / {:target="_blank"} {:target="_blank"} / {:target="_blank"} {:target="_blank"} {:target="_blank"} []({{ page.website }}/u/gallardoalba/h/mapping){:target="_blank"}
K-mer coverage []({{ page.website }}/u/delphine-l/w/kcov){:target="_blank"} []({{ page.website }}/u/delphine-l/h/kcov-1){:target="_blank"}
Salsa Scaffolding []({{ page.website }}/u/delphine-l/w/salsa-scaffolding){:target="_blank"} []({{ page.website }}/u/delphine-l/h/salsa-scaffolding){:target="_blank"}
Chloroplast genome assembly {:target="_blank"}
De Bruijn Graph Assembly {:target="_blank"}
Genome Assembly of MRSA using Illumina MiSeq Data {:target="_blank"}
Genome Assembly of MRSA using Oxford Nanopore MinION Data {:target="_blank"}
Making sense of a newly assembled genome {:target="_blank"}
Unicycler Assembly {:target="_blank"}
SARS-CoV-2 assembly with removing human reads {:target="_blank"}
{:.table.table-striped}

If you want to know more about the GTN or how to become part of the Galaxy community, check the videos below!

<iframe width="560" height="315" src="https://www.youtube.com/embed/lDqWxzWNk1k" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen> </iframe> <iframe width="560" height="315" src="https://www.youtube.com/embed/-1MPdxmRs8U" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

Partners

This service is a joint project between different groups from the Vertebrate Genomes Project (VGP){:target="_blank"}, the European Reference Genome Atlas project{:target="_blank"}, and the Galaxy project{:target="_blank"}. The service is part of the European Galaxy server and is maintained by the RNA Bioinformatics Center (RBC){:target="_blank"} as part of de.NBI{:target="_blank"} and ELIXIR{:target="_blank"}.

VGP ERGA