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
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
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

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 (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2 biodiversity
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 biodiversity apollo2

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 logoStéphanie Robin avatar Stéphanie Robinorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoErwan Corre avatar Erwan CorreYo Yehudi avatar Yo YehudiDaniela Butano avatar Daniela Butanoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoDeepti Varshney avatar Deepti VarshneyRobert Meller avatar Robert Mellerorcid logoAnna Syme avatar Anna SymeElizabeth Humphries avatar Elizabeth HumphriesBazante Sanders avatar Bazante SandersFrederick Tan avatar Frederick TanJasper Ouwerkerk avatar Jasper OuwerkerkNiall Beard avatar Niall Beardorcid logoHelena Rasche avatar Helena RascheNathan Dunn avatar Nathan Dunnorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoMaria Doyle avatar Maria Doyleorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoLaura Leroi avatar Laura LeroiTorsten Seemann avatar Torsten SeemannKatherine Cox avatar Katherine Coxorcid logoBérénice Batut avatar Bérénice BatutSimon Bray avatar Simon Brayorcid logoBjörn Grüning avatar Björn GrüningCandace Savonen avatar Candace Savonenorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMateo Boudet avatar Mateo BoudetAnton Nekrutenko avatar Anton NekrutenkoAva Hoffman avatar Ava Hoffmanorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoSimon Gladman avatar Simon Gladmanorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoAlexandre Cormier avatar Alexandre CormierNatalie Kucher avatar Natalie Kucherorcid logoPaul Zierep avatar Paul Ziereporcid logoTeresa Müller avatar Teresa Müllerorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jackson

Funding

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

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