Workflows

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.

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.