An intro to the new Ensembl and custom annotation with the

Ensembl Variant Effect Predictor (VEP)

Dr Jorge Batista da Rocha

Ensembl Outreach

QMUL EBI Visit July 2026

EMBL-EBI, Wellcome Genome Campus

https://training.ensembl.org/events/

European Molecular Biology Laboratory (EMBL)

https://www.embl.org/

https://training.ensembl.org/events/

European Bioinformatics Institute (EBI)

https://www.ebi.ac.uk/

https://training.ensembl.org/events/

Learning outcomes

• Differentiate the types of genomic data available in Ensembl
• Discover the list of species available via the Species Selector
• Explore genomic and variation data in Ensembl Beta via the apps
• Use the Ensembl Variant Effect Predictor (VEP) to annotate variants
• Describe common input formats for VEP
• Practice different command line options for VEP
• Understand where help and documentation is available

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https://training.ensembl.org/events/

Workshop structure

1. Presentation
1. What is the data / tool?
2. How do we produce / process the data?
2. Demonstration
1. Getting the data and using the tool
3. Exercises
1. Try things out for yourself and go beyond the demo
2. Remember: this is not a test!

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https://training.ensembl.org/events/

Materials

• Presentation slides
• Walk-throughs
• Exercises and answers

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training.ensembl.org

[paste Ensembl Training page URL here]

https://training.ensembl.org/events/

Agenda

Friday, 17^th July 2026 13:00 – 15:30 (ish)

13:00 – 13:35

• Introduction to Ensembl Beta
• Release Types on Beta
• Selecting genomes
• Exploring genomic regions
• Genes and transcripts

13:35 – 14:00

• Install check

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14:00 – 14:15

• Hydration Break

14:15 – 14:30

• Ensembl Variation and VEP (Brief)

14:30 – 15:20

• Follow along: Ensembl VEP Practical
• Wrap up and Feedback

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https://training.ensembl.org/events/

Health and Safety Info

• No fire alarms tests expected today
• If one rings we will evacuate back through entrance and assembly near car park
• There are exit doors to our left and right
• Toilets are on each floor, opposite reception entrance on this one
• There are also some upstairs
• Water is available in the kitchen and some snacks

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Introduction to Ensembl

Jorge Batista da Rocha

Ensembl Outreach

QMUL EBI Visit July 2026

EMBL-EBI, Wellcome Genome Campus

https://training.ensembl.org/events/

https://training.ensembl.org/events/

What is Ensembl?

Ensembl annotates and maps genomic features from genome sequences, and brings together information from a wide range of other databases in a single site.

AGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGTGCATTTTGGTCTTCTGTTTTGCAGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCTTGCTAAAAACCCAGTACGTCACAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACTAACAAATCAATTACTAAC

https://training.ensembl.org/events/

Ensembl features - Data available

• Genomes and gene builds for > 3000 species
• Genetic variation data
• Comparative genomics (homology tables)
• Regulatory builds
• More to come!

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https://training.ensembl.org/events/

Ensembl features - Powerful tools

• Tools - BLAST and Ensembl VEP
• Programmatic access via GraphQL and refget
• Completely open-source (FTP, GitHub)

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Access scales

Whole genome

Groups

One by one

Tools and APIs

FTP

VEP

Browser

NB! - Active development

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https://training.ensembl.org/events/

Ensembl Beta

• New Ensembl genome browser platform
• Highly responsive and modern user interface
• Browse multiple species of interest simultaneously
• All Ensembl sites now in a single platform

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• Currently under Beta testing – we want to hear your thoughts!

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https://training.ensembl.org/events/

Ensembl Beta Release cycle

Integrated Release

Partial

Release

Linkage Release

• Linked data frozen at a point in time

Data Release

• Assemblies
• Genesets
• Sequences

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• Regulation data
• Comparative genomics
• Linked data

https://training.ensembl.org/events/

Ensembl Beta Release cycle

Integrated Release

Partial

Releases

Selected Partial

3-4 Months

2 Weeks

https://training.ensembl.org/events/

Ensembl Beta Release cycle

Partial

Releases

2 Weeks

Next Integrated Release

Selected partial releases

3-4 Months

https://training.ensembl.org/events/

More information

Explore all help and documentation pages, including a guide to the new Ensembl browser.

Data- and tool-specific help pages.

Find out how the data was generated or how to use the tool.

Get in touch with the Ensembl Helpdesk.

Help & documentation

Help pages

Contact form

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Demonstration

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We are going to look at the Ensembl homepage, and learn how to find information about species and genome assemblies in Ensembl.

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[paste Ensembl Training page URL here]

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Use the Species Selector on https://beta.ensembl.org/ to look for your favourite animal species!

Species selector

https://training.ensembl.org/events/

Details in the species selector:

In the search result table:

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Details in the Species selector:

In the species page:

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Searching in the Species selector:

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Exploring genomic regions

https://training.ensembl.org/events/

Gene views in the Genome Browser App

Coding exon

Intron (reverse strand)

Non-coding exon

Intron (forward strand)

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Activity 1: Using the Genome Browser app to find a gene of interest

Genome browser

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Tracks in the Genome browser app

Genes you choose to view become a Focus entity

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Tracks in the Genome browser app

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Tracks are toggleable

Configure track details

Select types of tracks

Turn track views on / off

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Feedback

The site is in active development, so we welcome your feedback!

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We also gather feedback on this training - so please do take a moment to complete the feedback form on training.ensembl.org later!

https://training.ensembl.org/events/

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More information

Publication:

Aken BL, Ayling S, Barrell D, et al. The Ensembl gene annotation system. Database: the Journal of Biological Databases and Curation. 2016;2016. DOI:10.1093/database/baw093. PMID: 27337980; PMCID: PMC4919035.

Frankish A, Carbonell-Sala S, Diekhans M, et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. doi: 10.1093/nar/gkac1071. PMID: 36420896; PMCID: PMC9825462.

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https://www.ensembl.org/info/genome/genebuild/index.html

https://training.ensembl.org/events/

The Entity viewer

Learn more about a genetic feature (detailed gene, transcript and genetic variant information).

Entity viewer

https://training.ensembl.org/events/

The Entity viewer - Gene view

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Genetic variation

Ensembl Outreach

Jorge Batista da Rocha

https://training.ensembl.org/events/

Variant consequences

ATG

Regulatory feature

UTR

Intronic

Coding

(non-synonymous/�missense)

Coding

(synonymous)

Splice site

Upstream

UTR

Downstream

https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html

AAAAAA

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Variants in the Genome Browser

Please note - variants are not enabled in search as yet

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Variants in the Entity Viewer

https://training.ensembl.org/events/

Variants in the Entity Viewer

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More information

Publication:

Hunt SE, McLaren W, Gil L, et al. Ensembl variation resources. Database: the Journal of Biological Databases and Curation. 2018 Jan;2018. DOI: 10.1093/database/bay119. PMID: 30576484; PMCID: PMC6310513.

https://www.ensembl.org/info/genome/variation/index.html

https://training.ensembl.org/events/

The Ensembl Variant Effect Predictor (VEP)

Ensembl Outreach

Ensembl Genome Browser Workshop

Jorge Batista da Rocha

https://training.ensembl.org/events/

Ensembl VEP

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A tool to predict and annotate the functional consequences of variants.

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Variant Effect Predictor

https://training.ensembl.org/events/

Ensembl VEP interfaces

https://www.ensembl.org/info/docs/tools/vep/index.html

https://training.ensembl.org/events/

NB - VEP on Beta has limited functionality

Variant Effect Predictor

https://training.ensembl.org/events/

What can you do with the VEP? - current

https://training.ensembl.org/events/

What can you do with the VEP? - Beta

https://training.ensembl.org/events/

What can you do with the VEP? - Beta

https://training.ensembl.org/events/

Ensembl VEP interfaces

https://www.ensembl.org/info/docs/tools/vep/index.html

We’ll try this today:

Use web as backup

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More information

Publications:

Hunt SE, Moore B, Amode RM, et al. Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor - A tutorial. Human Mutation. 2022 Aug;43(8):986-997. DOI: 10.1002/humu.24298. PMID: 34816521; PMCID: PMC7613081.

McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome Biology. 2016 Jun;17(1):122. DOI: 10.1186/s13059-016-0974-4. PMID: 27268795; PMCID: PMC4893825.

https://www.ensembl.org/info/docs/tools/vep/index.html

https://training.ensembl.org/events/

Wrap-up

Jorge Batista da Rocha

Ensembl Outreach

https://training.ensembl.org/events/

https://training.ensembl.org/events/

https://training.ensembl.org/events/

Reach out to us

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/Ensembl.org

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@Ensembl

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/EnsemblGenomeBrowser

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www.ensembl.info

@ensembl

https://training.ensembl.org/events/

Help and documentation

Courses online https://www.ebi.ac.uk/training/

Tutorials https://www.ensembl.org/info/website/tutorials/

Flash animations https://www.youtube.com/user/EnsemblHelpdesk

https://youku.com/u/UMzM1NjkzMTI0

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Email helpdesk@ensembl.org

Mailing lists dev@ensembl.org

announce@ensembl.org

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Publications

• List of Ensembl publications:�https://www.ensembl.org/info/about/publications.html
• Topic-specific articles mentioned throughout the workshop

Harrison PW, Amode MR, Harrison PW, Austine-Orimoloye O et al. Ensembl 2024. Nucleic Acids Research. 2024 Jan;52(D1):D891-D899. DOI: 10.1093/nar/gkad1049. PMID: 37953337; PMCID: PMC10767893.

Yates AD, Allen J, Amode RM, et al. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research. 2022 Jan;50(D1):D996-D1003. DOI: 10.1093/nar/gkab1007. PMID: 34791415; PMCID: PMC8728113.

https://www.ensembl.org/info/about/publications.html

https://training.ensembl.org/events/

Acknowledgements and funding

National Human Genome Research Institute (NHGRI)

National Institute of Allergy and Infectious Diseases (NIAID)

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Training materials

• Ensembl training materials are protected by a CC BY license:�https://creativecommons.org/licenses/by/4.0/
• If you wish to re-use these materials, please credit Ensembl for their creation.
• If you use Ensembl for your work, please cite our papers:�https://www.ensembl.org/info/about/publications.html

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