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
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

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
Genomic Data Visualisation with JBrowse2
gmod jbrowse2

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 logoDelphine Lariviere avatar Delphine LariviereSimon Bray avatar Simon BrayBazante Sanders avatar Bazante SandersNathan Dunn avatar Nathan Dunnorcid logoStéphanie Robin avatar Stéphanie RobinNatalie Kucher avatar Natalie Kucherorcid logoLaura Leroi avatar Laura Leroiorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoDeepti Varshney avatar Deepti VarshneyDaniela Butano avatar Daniela ButanoKatherine Cox avatar Katherine Coxorcid logoMateo Boudet avatar Mateo BoudetNiall Beard avatar Niall BeardAnton Nekrutenko avatar Anton NekrutenkoAva Hoffman avatar Ava Hoffmanorcid logoPaul Zierep avatar Paul ZierepElizabeth Humphries avatar Elizabeth Humphriesorcid logoNicola Soranzo avatar Nicola SoranzoTorsten Seemann avatar Torsten Seemannorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoHelena Rasche avatar Helena Rascheorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoErwan Corre avatar Erwan Correorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoSimon Gladman avatar Simon Gladmanorcid logoMaria Doyle avatar Maria DoyleYo Yehudi avatar Yo YehudiCandace Savonen avatar Candace Savonenorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnna Syme avatar Anna SymeFrederick Tan avatar Frederick TanRobert Meller avatar Robert Mellerorcid logoBjörn Grüning avatar Björn Grüningorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoTeresa Müller avatar Teresa MüllerJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoMiaomiao Zhou avatar Miaomiao Zhou

Funding

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

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Avans
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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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ELIXIR Europe
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ABRomics
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NHGRI GDS Community Network
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The University of Melbourne
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NHGRI ANVIL
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IFB
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Melbourne Bioinformatics
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Australian BioCommons
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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.