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 ❌ ✅
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 23, 2025 2 ✅ ❌ ❌
Genome annotation with Prokka Genome Annotation with Prokka Aug 23, 2025 6 ✅ ❌ ❌
Identification of AMR genes in an assembled bacterial genome mrsa AMR gene detection Aug 23, 2025 1 ✅ ❌ ❌
Refining Genome Annotations with Apollo (prokaryotes) Apollo Load Test Aug 23, 2025 1 ❌ ❌ ❌
Essential genes detection with Transposon insertion sequencing Essential genes detection with Transposon insertion sequencing Aug 23, 2025 1 ✅ ❌ ❌
Comparison of two annotation tools - Helixer and Braker3 Comparison of two annotation tools: Helixer and Braker3 Aug 23, 2025 1 ✅ ✅ ✅
Genome annotation with Braker3 Genome annotation with Braker3 Aug 23, 2025 1 ✅ ✅ ✅
Genome annotation with Helixer annotation_helixer Aug 23, 2025 2 ✅ ✅ ✅
Masking repeats with RepeatMasker RepeatMasker Aug 23, 2025 1 ✅ ❌ ❌
Genome annotation with Funannotate Funannotate Aug 23, 2025 1 ✅ ❌ ❌
Genome annotation with Maker (short) Genome annotation with Maker (short) Aug 23, 2025 1 ❌ ❌ ❌
Genome annotation with Maker Genome annotation with Maker Aug 23, 2025 10 ❌ ❌ ❌
Functional annotation of protein sequences Functional annotation Aug 23, 2025 1 ✅ ❌ ❌
Long non-coding RNAs (lncRNAs) annotation with FEELnc Long non-coding RNAs (lncRNAs) annotation with FEELnc Aug 23, 2025 1 ❌ ❌ ❌
CRISPR screen analysis Workflow constructed from history 'CRISPR tutorial Kenji' Aug 23, 2025 1 ❌ ❌ ❌
From small to large-scale genome comparison CHROMEISTER chromosome comparison Aug 23, 2025 1 ❌ ❌ ❌
From small to large-scale genome comparison GECKO pairwise comparison Aug 23, 2025 1 ❌ ❌ ❌
Secondary metabolite discovery Gene Cluster Product Similarity Search Aug 23, 2025 1 ❌ ❌ ❌
Comparative gene analysis in unannotated genomes Comparative gene analysis Aug 23, 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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