| layout | subdomain |
|---|---|
subsite-galaxy |
erasmusmc |
Welcome to the Erasmus MC Galaxy webserver.
- TOC {:toc}
Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take a guided tour{:target="_blank"} through Galaxy's user interface.
Check also the standard but customizable workflows available there.
A collection of best practice and popular tools are integrated (and are expanding) in this custom Galaxy instance. The ONT-oriented and -specific subset includes:
- Polishing, QC and preprocessing
- {% include tool.html id="Porechop" %}, {% include tool.html id="Filtlong" %}, {% include tool.html id="Nanopolish" %}, {% include tool.html id="Poretools" %}
- Genome assembly
- {% include tool.html id="Minimap2" %}, {% include tool.html id="Miniasm" %}, {% include tool.html id="Racon" %}, {% include tool.html id="Racon" %}, {% include tool.html id="Flye" %}, {% include tool.html id="Unicycler" %}, {% include tool.html id="Wtdbg2" %}, {% include tool.html id="Canu" %}
- Mapping
- {% include tool.html id="Minimap2" %}, {% include tool.html id="GraphMap" %}
- Visualisation
- {% include tool.html id="Nanoplot" %}, {% include tool.html id="Bandage" %}
- Taxonomy and metagenomics
- {% include tool.html id="PlasFlow" %}, {% include tool.html id="Staramr" %}, {% include tool.html id="Kraken2" %}
We are passionate about training. So we are working in close collaboration with the Galaxy Training Network (GTN){:target="_blank"} to develop training materials of data analyses based on Galaxy {% cite batut2017community %}. The NanoGalaxy training materials are under development and will be soon hosted on the GTN GitHub repository https://training.galaxyproject.org{:target="_blank"}.
To orchestrate tools and help users with their analyses, some best practice workflows are prepared and become available. The workflows can be extended using similar and alternative combinations using the workflow editor.
The workflows are available in the Shared Workflows{:target="_top"}, with the label "ONT".
Some validated workflows:
- Basic workflows inspired by the Nanopolish tutorials
workflow{:target="_top"}
[workflow](https://nanopore.usegalaxy.eu/u/milad/w/ont-assembly-flye-ahrens){:target="_blank"}
- Unicycler-based WF for Klebsiella pneumoniae (Illumina and ONT) [Wick et al. Microbial genomics 2017]
Shared history: https://nanopore.usegalaxy.eu/u/milad/h/wick-etal
- Metagenomics: taxa classification
workflow{:target="_top"}
