Welcome to the ERGA Knowledge Hub - this is an open and global collection of educational resources in biodiversity genomics curated by the European Reference Genome Atlas Community. Submit and share resources to join our mission breaking down geographical barriers and facilitating knowledge transfer.

54 Resources

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CCGP Repository for the genome assembly working group.
Genome assembly Conservation genomics Unix/Linux Next generation sequencing
Days since last push
36 day(s)
License
-
biodiversity genomics course by Nicol Rueda, Karin Näsvall and Joana Meier from the Wellcome Sanger Institute
Genomics Next generation sequencing Comparative genomics Population genetics Phylogenetics / Phylogenomics
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85 day(s)
License
-
This repository contains course materials for a workshop on structural genome annotation with BRAKER and TSEBRA
Genome annotation
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377 day(s)
License
GNU General Public License v3.0
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
Assembly Evaluation Genome annotation
Days since last push
434 day(s)
License
MIT License
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
Genomics Transcriptomics
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473 day(s)
License
MIT License
A set of notes collected by the Coop lab in the area of Population Genetics
Authors
Population genetics
Days since last push
552 day(s)
License
MIT License
Explore the world of genome assembly and gain an understanding of the power and pitfalls of sequencing technologies and assembly techniques.
Genome assembly Genomics Long read sequencing High performance computing Next generation sequencing
Days since last push
602 day(s)
License
Creative Commons Zero v1.0 Universal
Authors
Genome assembly Unix/Linux High performance computing
Days since last push
617 day(s)
License
GNU General Public License v3.0
Genomics Variant analysis Comparative genomics
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1147 day(s)
License
Creative Commons Zero v1.0 Universal
Authors
Mark Ravinet, Joana Meier
Genomics Variant analysis Population genetics
Days since last push
-
License
MIT License
Authors
Hadrien Gourlé, Juliette Hayer, Oskar Karlsson, Jacques Dainat
High performance computing Genomics Genome assembly Genome annotation Next generation sequencing
Days since last push
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License
Creative Commons Attribution 4.0
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Authors
Delphine Lariviere, Alex Ostrovsky, Cristóbal Gallardo, Anna Syme, Linelle Abueg, Brandon Pickett, Giulio Formenti, Marcella Sozzoni, Anton Nekrutenko
Galaxy Genome assembly Long read sequencing
Days since last push
-
License
Creative Commons Attribution 4.0
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.
Authors
Anthony Bretaudeau
Genome annotation Galaxy
Days since last push
-
License
Creative Commons Attribution 4.0
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.
Authors
Anthony Bretaudeau
Galaxy Genome annotation
Days since last push
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License
Creative Commons Attribution 4.0
Genome bioinformatics: from short- to long-read sequencing materials 2023
Authors
Kayesha Coley, Chiara Batini, Charles Solomon, Maxime Tarabachi, Erik Garrison, Sean Laidlaw, Yo Yehudi, Daniel Thomas López, Louisse Mirabueno, Maira Ihsan, Dona Shaju
Next generation sequencing Long read sequencing Variant analysis Reproducibility Data management
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License
Creative Commons Attribution 4.0
https://BGA23.org/MitoHiFiAssembling Mitogenomes from PacBio HiFi reads using MitoHiFiThis session is part of Biodiversity Genomics Academy 2023Session Leade...
Authors
Marcela Uliano-Silva
Genomics Genome assembly Long read sequencing
Days since last push
-
License
Standard Youtube License
https://bga23.org/genomescopeGenome profiling using GenomeScopeThis session is part of Biodiversity Genomics Academy 2023Session Leader(s)Lucía Campos-Domíng...
Authors
Lucía Campos-Domínguez
Kamil Jaron
Genomics
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License
Standard Youtube License
Authors
Yannis Nevers
Genomics Genome annotation Comparative genomics
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License
Standard Youtube License
EMBL-EBI Train online course
Authors
Cath Brooksbank
Andrew Cowley
Data submission Database Management
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License
Creative Commons Attribution 4.0
EMBL-EBI Train online course
Authors
Data management FAIR data Reproducibility
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License
Creative Commons Attribution 4.0
EMBL-EBI Train online course
Authors

Emily Perry
Benjamin Moore
Helen Sparrow
Giulietta M. Spudich
Aleena Mushtaq
Genome annotation Database Management
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License
Creative Commons Attribution 4.0
EMBL-EBI Train online course
Authors

Sam Holt
Clara Amid
Maira Ihsan
Data management Data submission
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License
Creative Commons Attribution 4.0
EMBL-EBI Train online course
Authors
Laura Emery
Phylogenetics / Phylogenomics
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License
Creative Commons Attribution 4.0
Authors
Conservation genomics Genomics Next generation sequencing Population genetics
Days since last push
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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...
Authors
Dr Nandan Deshpande
RNA-seq Next generation sequencing Genome annotation
Days since last push
-
License
Creative Commons Attribution 4.0

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.

All material is:

  • Submitted and curated by the ERGA Community

  • Free to use with accreditation

Terms of use

Developed, maintained and curated by:

Yann Haefliger
Tom Brown
Diego De Panis
Luísa Marins
Christian de Guttry

Data last updated: 2024-12-04 01:01:41

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