Genome Annotation — Editorial Board Home

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Editorial Board

orcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSimon Gladman avatar Simon Gladman

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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 ❌ ❌ ❌ ✅ ❌
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 ❌ ✅ ❌ ✅ ❌
Creating an Official Gene Set ✅ ❌ ❌ ❌ ❌
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 Jan 15, 2025 2 ✅ ❌ ❌
Genome annotation with Prokka Genome Annotation with Prokka Jan 15, 2025 6 ✅ ❌ ❌
Identification of AMR genes in an assembled bacterial genome mrsa AMR gene detection Jan 15, 2025 1 ✅ ❌ ❌
Refining Genome Annotations with Apollo (prokaryotes) Apollo Load Test Jan 15, 2025 1 ❌ ❌ ❌
Essential genes detection with Transposon insertion sequencing Essential genes detection with Transposon insertion sequencing Jan 15, 2025 1 ✅ ❌ ❌
Genome annotation with Helixer annotation_helixer Jan 15, 2025 2 ✅ ✅ ✅
Masking repeats with RepeatMasker RepeatMasker Jan 15, 2025 1 ✅ ❌ ❌
Genome annotation with Funannotate Funannotate Jan 15, 2025 1 ✅ ❌ ❌
Genome annotation with Maker (short) Genome annotation with Maker (short) Jan 15, 2025 1 ❌ ❌ ❌
Genome annotation with Maker Genome annotation with Maker Jan 15, 2025 10 ❌ ❌ ❌
Functional annotation of protein sequences Functional annotation Jan 15, 2025 1 ✅ ❌ ❌
Long non-coding RNAs (lncRNAs) annotation with FEELnc Long non-coding RNAs (lncRNAs) annotation with FEELnc Jan 15, 2025 1 ❌ ❌ ❌
CRISPR screen analysis Workflow constructed from history 'CRISPR tutorial Kenji' Jan 15, 2025 1 ❌ ❌ ❌
From small to large-scale genome comparison CHROMEISTER chromosome comparison Jan 15, 2025 1 ❌ ❌ ❌
From small to large-scale genome comparison GECKO pairwise comparison Jan 15, 2025 1 ❌ ❌ ❌
Secondary metabolite discovery Gene Cluster Product Similarity Search Jan 15, 2025 1 ❌ ❌ ❌
Comparative gene analysis in unannotated genomes Comparative gene analysis Jan 15, 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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