Explore the ERGA Knowledge Hub, an open, global home for Biodiversity Genomics teaching resources curated by the European Reference Genome Atlas Community. Share your lectures, tutorials, workshops, or other learning tools in any language and help us bridge borders. Stand-alone manuals or pipelines are welcome only when paired with clear instructional guidance. Put simply: if your material teaches how, not just what, we want to feature it! Want to know more? Check out our short intro video.

108 Resources

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ebp-nor/workshop-2024
Authors
Genome annotation Genome assembly Comparative genomics
Last updated
2025-08-21
License
Creative Commons Attribution 4.0 International
Biodiversity Genomics Europe; SciLifeLab Hi-C Course - BGE + SciLifeLab Hi-C Course
Authors
Morten Skage, Irene Fabiola Roman Maldonado, Karine Labadie , Fernando Cruz Rodriguez, Graeme Oatley, Simona Buonanno, Lorenzo Ballini, Leonardo Girlanda and Annunziata De Luisi.
Skill level
Beginner
Genomics Epigenetics Long read sequencing
Submission date
2025-08-14
License
Creative Commons Attribution 4.0 International
Variant calling - sandbox.bio
Interactive bcftools and bowtie2 tutorial: learn to use variant calling to decode a secret message stored in sequencing data using a command-line interface in your browser.
Authors
Robert Aboukhalil
Skill level
Intermediate
Languages
en
English
Variant analysis
Submission date
2025-08-14
License
-
K-mer counting with Jellyfish - sandbox.bio
Interactive jellyfish tutorial: learn to perform k-mer counting using a command-line interface in your browser.
Authors
Robert Aboukhalil
Skill level
Beginner
Languages
en
English
Genome assembly
Submission date
2025-08-14
License
-
BLAST tutorial - sandbox.bio
Interactive BLAST tutorial: learn to align DNA and protein sequences using a command-line interface in your browser.
Authors
Shawn T. O’Neil
Skill level
Beginner
Languages
en
English
Genomics
Submission date
2025-08-14
License
Creative Commons Attribution 4.0 International
Tutorial: BAM parsing with samtools
Interactive samtools tutorial: learn to filter and wrangle SAM and BAM files using a command-line interface in your browser.
Authors
Aaron Quinlan
Skill level
Beginner
Languages
en
English
Genomics
Submission date
2025-08-14
License
-
IGV tutorial
This lab will introduce you to the Integrative Genomics Viewer (IGV), one of the most popular visualization tools for High Throughput Sequencing (HTS) data.
Authors
Malachi Griffith, Sorana Morrissy, Jim Robinson, Ben Ainscough, Jason Walker, and Obi Griffith
Skill level
Beginner
Languages
en
English
Data visualization
Submission date
2025-08-14
License
-
Bedtools tutorial - sandbox.bio
Interactive bedtools tutorial: learn to wrangle BED files using a command-line interface in your browser.
Authors
Aaron Quinlan
Skill level
Beginner
Languages
en
English
Genomics
Submission date
2025-08-14
License
-
Terminal Exercises - sandbox.bio
Interactive bash tutorial: learn to use the command line for bioinformatics data wrangling using a command-line interface in your browser.
Skill level
Intermediate
Languages
en
English
Unix/Linux
Submission date
2025-08-14
License
-
How to write a Bash script - sandbox.bio
Interactive Bash tutorial: learn to write your own Bash scripts and process user inputs using a command-line interface in your browser.
Authors
Robert Aboukhalil
Skill level
Beginner
Languages
en
English
Unix/Linux
Submission date
2025-08-14
License
-
Terminal Basics - sandbox.bio
Interactive bash tutorial: learn to get up to speed using a command-line interface in your browser.
Authors
Robert Aboukhalil
Skill level
Beginner
Languages
en
English
Unix/Linux
Submission date
2025-08-14
License
-
e-Aulas da USP :: Aula 6 parte 3, Sequenciamento de Nova Geração
Authors
Felipe Jun Fuzita
Next generation sequencing
Submission date
2025-08-14
License
-
Sequence alignment with bowtie2 - sandbox.bio
Interactive bowtie2 tutorial: learn to align sequencing reads to a reference genome using a command-line interface in your browser.
Authors
Ben Langmead
Skill level
Beginner
Next generation sequencing
Submission date
2025-08-14
License
Other
DNA sequencing QC - sandbox.bio
Interactive fastp tutorial: learn to evaluate the quality of FASTQ files from a sequencing run using a command-line interface in your browser.
Authors
Robert Aboukhalil
Skill level
Beginner
Next generation sequencing Quality Control
Submission date
2025-08-14
License
Other
Be FAIR and CARE - Core Principles for Open Science in Research with Objects - YouTube
Philipp Kandler, Open Science specialist at VuK Open Access Brandenburg, talks about FAIR principles, CARE principles, Open Science, PIDs, repositories and m...
Authors
Additional credit
Philipp Kandler
Languages
en
English
FAIR data Open Science
Upload date
2025-08-13
License
Standard Youtube License
rmwaterhouse/ERGA-Bitesize-BUSCO-genome
Genomics Quality Control with BUSCO - Genome Mode
Authors
Skill level
Beginner
Languages
en
English
Assembly Evaluation Quality Control
Last updated
2025-08-06
License
Creative Commons Attribution 4.0 International
BUSCO - from QC to gene prediction and phylogenomics
By the end of this session you will be able to: Understand the main uses of BUSCO in genomics Understand how BUSCO operates behind the scenes Run example assessments of genomic data with BUSCO Navigate your way around the main BUSCO outputs
Authors
Assembly Evaluation Genome annotation
Last updated
2025-08-06
License
MIT License
Methods in genomic variant calling | EMBL-EBI Training
EMBL-EBI Train online course
Authors
Tobias Rausch
Skill level
Beginner
Languages
en
English
Variant analysis
Submission date
2025-08-06
License
Creative Commons Attribution 4.0 International
Functional genomics I | EMBL-EBI Training
EMBL-EBI Train online course
Authors
Melissa Burke, Laura Huerta
Skill level
Beginner
Languages
en
English
Functional Genomics Reproducibility Genomics
Submission date
2025-08-06
License
Creative Commons Attribution 4.0 International
LEARN CitSci
Enhancing youth learning through Community and Citizen Science: a guide for practitioners
Authors
L Robinson; J Wardlaw; J Lorke; A Young; A miller; V burton; C herodotou; L higgins; G miller; M ghadiri khanaposhtani; A benavides lahnstein; H sanghera; M aristeidou; R johnso; H ballard; J jennewein; S pratt-taweh; N ismail; G pauly; T papathoma; R swanson;
Citizen Science
Submission date
2025-08-01
License
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0
Panel Seminars
Authors
Melanie LaCava, Alicia Mastretta-Yanes, Isaac Overcast, Jon Puritz, Jeffrey Good, Mikhail “Misha” Matz, Noah Reid, Tim Sackton, Nina Overgaard Therkildsen, Zach Gompert, Morgan Kelly, Katie Lotterhos, Jeff Ross-Ibarra, Ana Conesa, Sarah Davies, Martin Hölzer, Joanna Kelley, Harold Pimentel.
Genomics RNA-seq Population genetics Transcriptomics
Submission date
2025-08-01
License
Standard Youtube License
Data protection and privacy preservation in software development | EMBL-EBI Training
EMBL-EBI Train online course
Data science Data management
Submission date
2025-08-01
License
Creative Commons Attribution 4.0 International
Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics
Training material for all kinds of transcriptomics analysis.
Authors
Bérénice Batut Mallory Freeberg Mo Heydarian Anika Erxleben Pavankumar Videm Clemens Blank Maria Doyle Nicola Soranzo Peter van Heusden Lucille Delisle
Skill level
Beginner
RNA-seq Transcriptomics Quality Control Genomics
Submission date
2025-08-01
License
Creative Commons Attribution 4.0 International
FAIR-by-Design Methodology
Skills4EOSC ‘Skills for the European Open Science commons: creating a training ecosystem for Open and FAIR science’ is funded by the European Commission Horizon Europe programme. Coordinated by Consortium GARR and supported by 44 partners in 18 European countries.
FAIR data Educational resources Training
Submission date
2025-07-01
License
Creative Commons Attribution 4.0 International
rapidspeciation/biodiversity_genomics_course
biodiversity genomics course by Nicol Rueda, Karin Näsvall and Joana Meier from the Wellcome Sanger Institute
Authors
Genomics Next generation sequencing Comparative genomics Population genetics Phylogenetics / Phylogenomics
Last updated
2025-06-08
License
-

About

The ERGA Knowledge Hub is a list of training material and resources related to biomaterial sampling, reference genome generation, analysis, teaching, and legal and ethical aspects, curated by the community of the European Reference Genome Atlas. This initiative was made possible thanks to Biodiversity Genomics Europe (BGE) funded by the European Union under the Horizon Europe research and innovation program, co-funded by the Swiss and British governments.

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