Genome Annotation — Editorial Board Home

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orcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Introduction to Genome Annotation ❌ ✅
Bacterial Genome Annotation ✅ ✅ ✅
Genome Annotation ✅ ✅
Genome annotation with Prokka ❌ ✅ ✅
Identification of AMR genes in an assembled bacterial genome ✅ ✅ ✅
Refining Genome Annotations with Apollo (prokaryotes) ✅ ✅ ✅
Essential genes detection with Transposon insertion sequencing ❌ ✅
Comparison of two annotation tools - Helixer and Braker3 ✅ ✅ ✅
Genome annotation with Braker3 ✅ ✅ ✅
Genome annotation with Helixer ✅ ✅ ✅
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 ❌ ✅ ✅
Bacterial genome quality control ✅ ✅
Bacterial pangenomics ✅ ✅
Creating an Official Gene Set ✅ ❌
Dataset construction for bacterial comparative genomics ✅ ✅
From small to large-scale genome comparison ❌ ✅ ✅
Secondary metabolite discovery ❌ ✅
Comparative gene analysis in unannotated genomes ❌ ✅ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Bacterial Genome Annotation Bacterial Genome Annotation Aug 3, 2025 2 ✅ ❌ ❌
Genome annotation with Prokka Genome Annotation with Prokka Aug 3, 2025 6 ✅ ❌ ❌
Identification of AMR genes in an assembled bacterial genome mrsa AMR gene detection Aug 3, 2025 1 ✅ ❌ ❌
Refining Genome Annotations with Apollo (prokaryotes) Apollo Load Test Aug 3, 2025 1 ❌ ❌ ❌
Essential genes detection with Transposon insertion sequencing Essential genes detection with Transposon insertion sequencing Aug 3, 2025 1 ✅ ❌ ❌
Comparison of two annotation tools - Helixer and Braker3 Comparison of two annotation tools: Helixer and Braker3 Aug 3, 2025 1 ✅ ✅ ✅
Genome annotation with Braker3 Genome annotation with Braker3 Aug 3, 2025 1 ✅ ✅ ✅
Genome annotation with Helixer annotation_helixer Aug 3, 2025 2 ✅ ✅ ✅
Masking repeats with RepeatMasker RepeatMasker Aug 3, 2025 1 ✅ ❌ ❌
Genome annotation with Funannotate Funannotate Aug 3, 2025 1 ✅ ❌ ❌
Genome annotation with Maker (short) Genome annotation with Maker (short) Aug 3, 2025 1 ❌ ❌ ❌
Genome annotation with Maker Genome annotation with Maker Aug 3, 2025 10 ❌ ❌ ❌
Functional annotation of protein sequences Functional annotation Aug 3, 2025 1 ✅ ❌ ❌
Long non-coding RNAs (lncRNAs) annotation with FEELnc Long non-coding RNAs (lncRNAs) annotation with FEELnc Aug 3, 2025 1 ❌ ❌ ❌
CRISPR screen analysis Workflow constructed from history 'CRISPR tutorial Kenji' Aug 3, 2025 1 ❌ ❌ ❌
From small to large-scale genome comparison CHROMEISTER chromosome comparison Aug 3, 2025 1 ❌ ❌ ❌
From small to large-scale genome comparison GECKO pairwise comparison Aug 3, 2025 1 ❌ ❌ ❌
Secondary metabolite discovery Gene Cluster Product Similarity Search Aug 3, 2025 1 ❌ ❌ ❌
Comparative gene analysis in unannotated genomes Comparative gene analysis Aug 3, 2025 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
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TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

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