index-nanopore.md

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subsite-galaxy	nanopore

Welcome to NanoGalaxy -- a webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies.

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{:target="_blank"} through Galaxy's user interface.

Check also the standard but customizable workflows available there.

Tools

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:

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<div align="center"> <b>Polishing, QC and preprocessing</b><br/> <br/> {% include tool.html id="Porechop" %}, {% include tool.html id="Filtlong" %}, {% include tool.html id="Nanopolish" %}, {% include tool.html id="Poretools" %}, {% include tool.html id="Medaka" %}, {% include tool.html id="MultiQC" %} </div> </th> <th class="tg-0lax" rowspan="4" align="center"> <img src="/assets/media/nanogalaxy_toolkit.png" height="400px" alt="NanoGalaxy toolkit"/> </th>
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" %}
Visualisation {% include tool.html id="Nanoplot" %}, {% include tool.html id="Bandage" %} </div> </td>
Taxonomy and metagenomics {% include tool.html id="PlasFlow" %}, {% include tool.html id="Staramr" %}, {% include tool.html id="Kraken2" %} </div> </td>

Tutorials

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 %}. These materials hosted on the GTN GitHub repository are available online at https://training.galaxyproject.org{:target="_blank"}.

Workflows

To orchestrate tools and help users with their analyses, some best practice workflows are prepared and available for all users. The workflows can be extended using similar and alternative combinations using the Galaxy workflow editor.

The workflows are available in the Shared Workflows View{:target="_top"} and are labeled with "ONT".

|:-----------------:|:----------------------------:|:-------------------:|:------------------:| | | | | | | {:target="_top"} | {:target="_blank"} | {:target="_blank"} | {:target="_top"} | | Basic workflows inspired by the Nanopolish tutorials | Genome assembly: Flye-based WF for highly repetitive genomes [Schmid et al. NAR 2018] | Genome assembly: Unicycler-based WF for Klebsiella pneumoniae [Wick et al. Microbial genomics 2017] | Metagenomics: taxa classification| | | | | | {:.table-striped .ont-workflow-table}

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