Galaxy

The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.

These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!

This team and associated Galaxy workflows are maintained by the European Galaxy Team.

The Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.

You can contribute too!

Reference data to beused with https://workflowhub.eu/workflows/1260

Post-curation processing workflow for VGP assemblies. Takes a curated AGP file and combined haplotype FASTA, splits by haplotype, applies curation, assigns chromosome names, renames and reorients hap2 to match hap1, then generates QC outputs including Compleasm, Pretext maps, telomere analysis, and coverage tracks.

This workflow performs colour deconvolution and automated thresholding to quantify stained area in brightfield histological images (MT, IHC). It accepts whole slides or pre-cropped ROIs.

A comprehensive Galaxy workflow for the end-to-end analysis of transcriptomics data, featuring automated QC, clustering, spatial statistics, cell type annotation, and cell-cell communication.

Metaproteomics 101 tutorial

Associated Tutorial

This workflows is part of the tutorial Metaproteomics tutorial, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...

This WF applies Flexynesis on BRCA data from Metabric for a classification task

Associated Tutorial

This workflows is part of the tutorial Modeling Breast Cancer Subtypes with Flexynesis, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Regression in Machine Learning

Associated Tutorial

This workflows is part of the tutorial Regression in Machine Learning, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...

22_04_30: WF Update

The workflow serves as a short introduction to Galaxy for users from the Humanities who mostly work with texts.

Associated Tutorial

This workflows is part of the tutorial Introduction to Digital Humanities in Galaxy, available in the GTN

Features

• Includes [Galaxy Workflow ...

Workflow used for the Ecology tutorial devoted to use yolo model on SEANOE marine data

Associated Tutorial

This workflows is part of the tutorial Object detection with YOLO, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a ...

V 20 Renamed several output datasets in workflow

Associated Tutorial

This workflows is part of the tutorial Text-Mining Differences in Chinese Newspaper Articles, available in the GTN

Features

• Includes a Galaxy Workflow Report
• Uses ...

Text mining a museum collection in tabular format to extract from which year most objects derive and what they are.

Version 2, including updated tools from 05/2026.

Text mining a museum collection in tabular format to extract from which year most objects derive and what they are.

Associated Tutorial

This workflows is part of the tutorial OpenRefine Tutorial for researching cultural data, available in the GTN

Features

• Includes [Galaxy Workflow ...

Evaluation of Pacbio Hifi Reads and genome profiling. Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

Associated Tutorial

This workflows is part of the tutorial Assembly of the mitochondrial genome from PacBio HiFi reads, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): VGP, Galaxy

**Tutorial ...

Associated Tutorial

This workflows is part of the tutorial Proteogenomics 2: Database Search, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a Galaxy Workflow Report ...

This Workflow transcribes a video or audio with multiple speakers. After transcription, it allocates the names of the speakers and groups and cleans passages from the two main speakers for further analysis.

Associated Tutorial

This workflows is part of the tutorial Transcribing Audio and Video files with Automated Speech Recognition, available in the ...

Train and evaluate a HANCOCK recurrence model with Multimodal Learner

Associated Tutorial

This workflows is part of the tutorial Gleam Multimodal Learner - Head and Neck cancer Recurrence Prediction with HANCOCK, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

This workflow performs functional annotation of protein and nucleotide sequences (including CDS, genomes and metagenomes) using eggNOG-mapper and InterProScan, supports collection inputs and optional analysis steps, and can assess KEGG pathway completeness.

Associated Tutorial

This workflows is part of the tutorial Introduction to Galaxy as an RDM platform, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a Galaxy Workflow Report ...

This workflow performs automated, parallel annotation of metagenome-assembled genomes (MAGs) to generate standardized annotation outputs, merged summary tables, and integrated quality reports across all genomes.

Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.