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:

Yo Yehudi avatar Yo Yehudiorcid logoBérénice Batut avatar Bérénice Batutorcid logoErwan Corre avatar Erwan CorreDaniela Butano avatar Daniela Butanoorcid logoMaria Doyle avatar Maria DoyleFrederick Tan avatar Frederick TanTorsten Seemann avatar Torsten SeemannNiall Beard avatar Niall Beardorcid logoMateo Boudet avatar Mateo BoudetAva Hoffman avatar Ava Hoffmanorcid logoSaskia Hiltemann avatar Saskia HiltemannSimon Bray avatar Simon Brayorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoTeresa Müller avatar Teresa Müllerorcid logoPaul Zierep avatar Paul Ziereporcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoLaura Leroi avatar Laura Leroiorcid logoBjörn Grüning avatar Björn Grüningorcid logoDeepti Varshney avatar Deepti VarshneyRobert Meller avatar Robert Mellerorcid logoAnthony Bretaudeau avatar Anthony BretaudeauElizabeth Humphries avatar Elizabeth Humphriesorcid logoJonathan Kreplak avatar Jonathan KreplakAnton Nekrutenko avatar Anton NekrutenkoKatherine Cox avatar Katherine CoxJasper Ouwerkerk avatar Jasper OuwerkerkNatalie Kucher avatar Natalie Kucherorcid logoAnna Syme avatar Anna SymeBazante Sanders avatar Bazante Sandersorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSimon Gladman avatar Simon GladmanNathan Dunn avatar Nathan Dunnorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoHelena Rasche avatar Helena RascheCandace Savonen avatar Candace Savonenorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoNicola Soranzo avatar Nicola Soranzoorcid 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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Melbourne Bioinformatics
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NHGRI GDS Community Network
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ABRomics
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IFB
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Avans
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The University of Melbourne
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NHGRI ANVIL
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ELIXIR Europe
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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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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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Australian BioCommons