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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.
22 Resources
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Date
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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
github
Assembly Evaluation
Genome annotation
Last updated
2025-08-06
License
MIT License
Training material for all kinds of transcriptomics analysis.
website
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
The playlist gathers the videos recorded during the SIB course “NGS - Genome Variant Analysis” streamed on 05-06 Sep 2023. In this two-day course we will cov...
website
Authors
Geert van Geest
Variant analysis
Genome annotation
Submission date
2025-03-24
License
Creative Commons Attribution 4.0 International
Authors
Laura Huerta, Melissa Burke, Flaminia Zane
Functional Genomics
Genomics
Next generation sequencing
RNA-seq
Pathways and Networks
Epigenetics
Submission date
2025-03-24
License
Creative Commons Attribution-NonCommercial 4.0
Plant genomes: from data to discovery
website
Genomics
Data management
Data submission
Variant analysis
Transcriptomics
FAIR data
Assembly Evaluation
Submission date
2024-12-16
License
Creative Commons Attribution 4.0 International
Thorough guide for annotating and masking repeats using RepeatModeler/RepeatMasker.
website
Authors
Daren Card
Genome annotation
Submission date
2024-10-24
License
MIT License
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
website
Authors
Romane Libouban, Anthony Bretaudeau
Genomics
Galaxy
Genome annotation
Submission date
2024-10-14
License
Creative Commons Attribution 4.0 International
Annotating genomes the Ensembl way is presented by Vianey Paola Barrera Enriquez, Jose Perez-Silva and Swati Sinha.This session is split into two parts:Part ...
website
Authors
Vianey Paola Barrera Enriquez, Jose Perez-Silva and Swati Sinha.
Genome annotation
RNA-seq
Quality Control
Last updated
2024-10-02
License
Standard Youtube License
Authors
Leanne Haggerty
Swati Sinha
Swati Sinha
Genome annotation
Submission date
2024-09-11
License
Standard Youtube License
A walk-through of a manual curation technique for genome assembly
website
Authors
Camilla Ryan
Genome assembly
Assembly Curation
Genomics
Submission date
2024-08-23
License
-
Rfam is a database of RNA families that currently contains over 4,000 families. Together with the Infernal software, Rfam is commonly used to annotate non-coding RNAs in newly sequenced genomes.
This webinar gives an overview of the data available in Rfam and give a live demo of annotating a genome with non-coding RNAs using Rfam and the Infernal software.
website
Authors
Emma Cooke, Nancy Ontiveros, Blake Sweeney, Sam Griffiths-Jones
Genome annotation
Genomics
Database Management
Submission date
2024-07-29
License
Creative Commons Attribution 4.0 International
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.
website
Authors
Anthony Bretaudeau, Helena Rasche, Alexandre Cormier, Laura Leroi, Erwan Corre, Stéphanie Robin, Jonathan Kreplak
Genome annotation
Galaxy
Genomics
Submission date
2024-06-06
License
Creative Commons Attribution 4.0 International
Authors
Emily Perry
Benjamin Moore
Helen Sparrow
Giulietta M. Spudich
Aleena Mushtaq
Genome annotation
Database Management
Submission date
2024-06-05
License
Creative Commons Attribution 4.0 International
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
website
Authors
Anthony Bretaudeau
Galaxy
Genome annotation
Submission date
2024-06-04
License
Creative Commons Attribution 4.0 International
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
website
Authors
Anthony Bretaudeau
Genome annotation
Galaxy
Submission date
2024-06-04
License
Creative Commons Attribution 4.0 International
Authors
Hadrien Gourlé, Juliette Hayer, Oskar Karlsson, Jacques Dainat
High performance computing
Genomics
Genome assembly
Genome annotation
Next generation sequencing
Submission date
2024-06-03
License
Creative Commons Attribution 4.0 International
This repository contains course materials for a workshop on structural genome annotation with BRAKER and TSEBRA
github
Authors
Genome annotation
Last updated
2023-11-22
License
GNU General Public License v3.0
An introduction and summary of Earl Grey - A user-friendly and fully automated TE annotation pipeline to steamline TE curation and annotation in diverse geno...
website
Authors
Tobias Baril
Genomics
Genome annotation
Last updated
2023-11-13
License
Standard Youtube License
Authors
Yannis Nevers
Genomics
Genome annotation
Comparative genomics
Last updated
2023-09-17
License
Standard Youtube License
RNA sequencing (RNAseq) is a powerful technique for investigating gene expression in biological samples. Processing and analysing RNAseq data involves multip...
website
Authors
Dr Nandan Deshpande
RNA-seq
Next generation sequencing
Genome annotation
Last updated
2023-09-07
License
Creative Commons Attribution 4.0 International
By the end of this session, you will be able to:
Structurally and functionally annotate a eukaryotic genome assembly with EASEL using protein and RNA extrinsic evidence
Assess non-model genome annotation quality with BUSCO score, mono:multi-exonic ratio, and reciprocal BLAST annotation rate
Address challenges with accuracy and efficiency for genome annotation
github
Genomics
Transcriptomics
Last updated
2023-08-18
License
MIT License
Every year, the students attending Introduction to Bioinformatics have the opportunity to listen to experts working in this field.In the second session, Tyle...
website
Authors
Tyler Alioto
Genomics
Genome annotation
Genome assembly
Last updated
2022-10-19
License
Standard Youtube License
Topics