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

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.

This workflow performs variant and genotype calling on whole-genome paired-end sequencing data from organisms of any ploidy to produce annotated VCF and TSV files

Runs CAPHEINE selection analyses with optional foreground/background branch labeling for branch comparisons.

This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format.

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.

Basic workflow to upload images into OMERO together with ROIs

Associated Tutorial

This workflows is part of the tutorial Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy, available in the GTN

Features

• Includes a Galaxy Workflow Report ...

Associated Tutorial

This workflows is part of the tutorial Segmentation of Anatomical Structures in Medical 3-D Images, available in the GTN

Features

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

This workflow performs multi-algorithm metagenomic binning evaluation using CONCOCT, MetaBAT2, SemiBin, and MaxBin2, optimizes results with DAS Tool and Binette, and evaluates all binning outputs against a gold standard using the CAMI AMBER framework to generate comprehensive HTML reports and performance metrics.

This workflow performs taxonomic classification of an input sequence collection (e.g., bins from SemiBin2 or MetaBat) using GTDB-Tk and maps the resulting taxonomy to NCBI taxIDs and names to reconcile differences between classification systems.

An example how ISCC codes can be used to verify image analysis steps

Associated Tutorial

This workflows is part of the tutorial Content Tracking and Verification in Galaxy Workflows with ISCC-SUM, available in the GTN

Features

• Includes Galaxy Workflow Tests

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This workflow is executing a BiaPy workflow using a YAML file where the model selection is predefined.

Associated Tutorial

This workflows is part of the tutorial Execute a BiaPy workflow in Galaxy, available in the GTN

Features

• Includes Galaxy Workflow Tests

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Associated Tutorial

This workflows is part of the tutorial GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000, available in the GTN

Features

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

Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5).

Purge contigs marked as duplicates by purge_dups.

This workflow starts from metagenomics short-read data and performs, taxonomic profiling (using Sylph), predicts Antibiotic Resistance Genes (ARGs) (using Groot and deepARG), and standardizes ARG annotations (using argNorm).