Genome Annotation — Editorial Board Home

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orcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHelena Rasche avatar Helena Rasche

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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Introduction to Genome Annotation ❌ ✅
Essential genes detection with Transposon insertion sequencing ❌ ✅
Bacterial Genome Annotation ✅ ✅ ✅
Genome Annotation ✅ ✅
Genome annotation with Prokka ✅ ✅ ✅
Identification of AMR genes in an assembled bacterial genome ✅ ✅ ✅
Refining Genome Annotations with Apollo (prokaryotes) ✅ ✅ ✅
Masking repeats with RepeatMasker ✅ ✅ ✅
Genome annotation with Funannotate ✅ ✅ ✅ ✅
Genome annotation with Maker (short) ❌ ✅
Genome annotation with Maker ❌ ✅
Functional annotation of protein sequences ✅ ✅
Refining Genome Annotations with Apollo (eukaryotes) ✅ ✅ ✅
Long non-coding RNAs (lncRNAs) annotation with FEELnc ✅ ✅ ✅
CRISPR screen analysis ❌ ✅ ✅
Comparison of two annotation tools - Helixer and Braker3 ✅ ✅ ✅
Genome annotation with Braker3 ✅ ✅ ✅
Genome annotation with Helixer ✅ ✅ ✅
Comparative gene analysis in unannotated genomes ❌ ✅ ✅
Bacterial genome quality control ✅ ❌
Bacterial pangenomics ✅ ❌
Creating an Official Gene Set ✅ ❌
Dataset construction for bacterial comparative genomics ✅ ❌
From small to large-scale genome comparison ❌ ✅ ✅
Pangenome analysis with Roary ✅ ✅
Secondary metabolite discovery ❌ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Essential genes detection with Transposon insertion sequencing Essential genes detection with Transposon insertion sequencing Oct 9, 2026 1 ✅ ❌ ❌
Bacterial Genome Annotation Bacterial Genome Annotation Oct 9, 2026 2 ✅ ❌ ❌
Genome annotation with Prokka Genome Annotation with Prokka Oct 9, 2026 6 ✅ ❌ ❌
Identification of AMR genes in an assembled bacterial genome mrsa AMR gene detection Oct 9, 2026 2 ✅ ✅ ❌
Refining Genome Annotations with Apollo (prokaryotes) Apollo Load Test Oct 9, 2026 1 ❌ ❌ ❌
Masking repeats with RepeatMasker RepeatMasker Oct 9, 2026 1 ✅ ❌ ❌
Genome annotation with Funannotate Funannotate Oct 9, 2026 1 ✅ ❌ ❌
Genome annotation with Maker (short) Genome annotation with Maker (short) Oct 9, 2026 1 ❌ ❌ ❌
Genome annotation with Maker Genome annotation with Maker Oct 9, 2026 10 ❌ ❌ ❌
Functional annotation of protein sequences Functional annotation Oct 9, 2026 1 ✅ ❌ ❌
Long non-coding RNAs (lncRNAs) annotation with FEELnc Long non-coding RNAs (lncRNAs) annotation with FEELnc Oct 9, 2026 1 ❌ ❌ ❌
CRISPR screen analysis Workflow constructed from history 'CRISPR tutorial Kenji' Oct 9, 2026 1 ❌ ❌ ❌
Comparison of two annotation tools - Helixer and Braker3 Comparison of two annotation tools: Helixer and Braker3 Oct 9, 2026 1 ✅ ✅ ✅
Genome annotation with Braker3 Genome annotation with Braker3 Oct 9, 2026 1 ✅ ✅ ✅
Genome annotation with Helixer annotation_helixer Oct 9, 2026 2 ✅ ✅ ✅
Comparative gene analysis in unannotated genomes Comparative gene analysis Oct 9, 2026 1 ❌ ❌ ❌
From small to large-scale genome comparison CHROMEISTER chromosome comparison Oct 9, 2026 1 ❌ ❌ ❌
From small to large-scale genome comparison GECKO pairwise comparison Oct 9, 2026 1 ❌ ❌ ❌
Secondary metabolite discovery Gene Cluster Product Similarity Search Oct 9, 2026 1 ❌ ❌ ❌

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Learning Pathways using materials from this Topic

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Detection of AMR genes in bacterial genomes

This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.

amr bacteria microgalaxy one-health microbiome
Galaxy Genome Annotation logo
Genome annotation for eukaryotes

Learn how to annotate an eukaryotic genome sequence: identify repeated regions, find the position and function of genes, and even set up a manual curation environment with Apollo.

genome-annotation eukaryote
Galaxy Genome Annotation logo
Genome annotation for prokaryotes

Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo.

genome-annotation prokaryote
MAG logo
Building and Annotating Metagenome-Assembled Genomes (MAGs) from Metagenomics Reads

This learning path will guide you through the process of constructing and analyzing Metagenome-Assembled Genomes (MAGs) using the Galaxy platform. You will explore the key steps involved in transforming raw metagenomic data into high-quality MAGs, from preprocessing to functional annotation. By the end of this path, you will be able to: List and describe the essential steps in MAGs construction,...

microbiome
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TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

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