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 Jul 17, 2025 2 ✅ ❌ ❌
Genome annotation with Prokka Genome Annotation with Prokka Jul 17, 2025 6 ✅ ❌ ❌
Identification of AMR genes in an assembled bacterial genome mrsa AMR gene detection Jul 17, 2025 1 ✅ ❌ ❌
Refining Genome Annotations with Apollo (prokaryotes) Apollo Load Test Jul 17, 2025 1 ❌ ❌ ❌
Essential genes detection with Transposon insertion sequencing Essential genes detection with Transposon insertion sequencing Jul 17, 2025 1 ✅ ❌ ❌
Comparison of two annotation tools - Helixer and Braker3 Comparison of two annotation tools: Helixer and Braker3 Jul 17, 2025 1 ✅ ✅ ✅
Genome annotation with Braker3 Genome annotation with Braker3 Jul 17, 2025 1 ✅ ✅ ✅
Genome annotation with Helixer annotation_helixer Jul 17, 2025 2 ✅ ✅ ✅
Masking repeats with RepeatMasker RepeatMasker Jul 17, 2025 1 ✅ ❌ ❌
Genome annotation with Funannotate Funannotate Jul 17, 2025 1 ✅ ❌ ❌
Genome annotation with Maker (short) Genome annotation with Maker (short) Jul 17, 2025 1 ❌ ❌ ❌
Genome annotation with Maker Genome annotation with Maker Jul 17, 2025 10 ❌ ❌ ❌
Functional annotation of protein sequences Functional annotation Jul 17, 2025 1 ✅ ❌ ❌
Long non-coding RNAs (lncRNAs) annotation with FEELnc Long non-coding RNAs (lncRNAs) annotation with FEELnc Jul 17, 2025 1 ❌ ❌ ❌
CRISPR screen analysis Workflow constructed from history 'CRISPR tutorial Kenji' Jul 17, 2025 1 ❌ ❌ ❌
From small to large-scale genome comparison CHROMEISTER chromosome comparison Jul 17, 2025 1 ❌ ❌ ❌
From small to large-scale genome comparison GECKO pairwise comparison Jul 17, 2025 1 ❌ ❌ ❌
Secondary metabolite discovery Gene Cluster Product Similarity Search Jul 17, 2025 1 ❌ ❌ ❌
Comparative gene analysis in unannotated genomes Comparative gene analysis Jul 17, 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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