GMOD

Tutorials from the world of the Generic Model Organism Database (GMOD)

GMOD is a collection of open source software tools for managing, visualising, storing, and disseminating genetic and genomic data, many of which are directly interoperable.

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Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

JBrowse 1

Learn to use JBrowse v1 here.

Lesson Slides Hands-on Recordings Input dataset Workflows
Bacterial Genome Annotation
gmod illumina bacteria microgalaxy jbrowse1
Genome annotation with Prokka
gmod prokaryote microgalaxy jbrowse1
Genomic Data Visualisation with JBrowse
gmod jbrowse1
Identification of AMR genes in an assembled bacterial genome
gmod illumina amr one-health jbrowse1 microgalaxy biodiversity
Making sense of a newly assembled genome
gmod prokaryote microgalaxy jbrowse1
Microbial Variant Calling
prokaryote microgalaxy gmod jbrowse1
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 biodiversity apollo2
SARS-CoV-2 Viral Sample Alignment and Variant Visualization
covid19 gmod jbrowse1
Genome annotation with Funannotate
gmod eukaryote jbrowse1 biodiversity
Genome annotation with Maker (short)
gmod eukaryote maker jbrowse1
Genome annotation with Maker
gmod eukaryote jbrowse1 maker
Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2 biodiversity

MAKER

Genome Annotation with MAKER.

Lesson Slides Hands-on Recordings Input dataset Workflows
Genome annotation with Maker (short)
gmod eukaryote maker jbrowse1
Genome annotation with Maker
gmod eukaryote jbrowse1 maker

InterMine

InterMine is a data warehouse you can query for interesting features and data.

Lesson Slides Hands-on Recordings Input dataset Workflows
InterMine integration with Galaxy
gmod intermine

Apollo v2

Apollo is a collaborative, real time genome annotation editor.

Lesson Slides Hands-on Recordings Input dataset Workflows
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 biodiversity apollo2
Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2 biodiversity

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Contributors

This material was contributed to by:

orcid logoMateo Boudet avatar Mateo Boudetorcid logoSaskia Hiltemann avatar Saskia HiltemannAva Hoffman avatar Ava HoffmanCandace Savonen avatar Candace Savonenorcid logoPaul Zierep avatar Paul Ziereporcid logoBérénice Batut avatar Bérénice BatutNathan Dunn avatar Nathan Dunnorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDelphine Lariviere avatar Delphine LariviereNatalie Kucher avatar Natalie KucherKatherine Cox avatar Katherine CoxDaniela Butano avatar Daniela Butanoorcid logoLaura Leroi avatar Laura Leroiorcid logoErwan Corre avatar Erwan Correorcid logoHelena Rasche avatar Helena RascheSimon Bray avatar Simon BrayTorsten Seemann avatar Torsten Seemannorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoSimon Gladman avatar Simon Gladmanorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnton Nekrutenko avatar Anton Nekrutenkoorcid logoTeresa Müller avatar Teresa Müllerorcid logoAnna Syme avatar Anna SymeElizabeth Humphries avatar Elizabeth HumphriesJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoMiaomiao Zhou avatar Miaomiao ZhouRobert Meller avatar Robert MellerYo Yehudi avatar Yo YehudiFrederick Tan avatar Frederick TanBazante Sanders avatar Bazante Sandersorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoBjörn Grüning avatar Björn Grüning

Funding

These individuals or organisations provided funding support for the development of this resource

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NHGRI ANVIL
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ABRomics
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
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ELIXIR Europe
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NHGRI GDS Community Network
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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.
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Avans
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IFB