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:

Jasper Ouwerkerk avatar Jasper OuwerkerkNathan Dunn avatar Nathan Dunnorcid logoHelena Rasche avatar Helena Rascheorcid logoCristóbal Gallardo avatar Cristóbal GallardoNatalie Kucher avatar Natalie Kucherorcid logoBérénice Batut avatar Bérénice Batutorcid logoDelphine Lariviere avatar Delphine LariviereAnton Nekrutenko avatar Anton NekrutenkoDaniela Butano avatar Daniela Butanoorcid logoMiaomiao Zhou avatar Miaomiao ZhouSimon Bray avatar Simon Brayorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoTeresa Müller avatar Teresa MüllerRobert Meller avatar Robert Mellerorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoNicola Soranzo avatar Nicola SoranzoElizabeth Humphries avatar Elizabeth Humphriesorcid logoTristan Reynolds avatar Tristan ReynoldsKatherine Cox avatar Katherine Coxorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMateo Boudet avatar Mateo BoudetYo Yehudi avatar Yo YehudiCandace Savonen avatar Candace Savonenorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBazante Sanders avatar Bazante Sandersorcid logoMaria Doyle avatar Maria DoyleTorsten Seemann avatar Torsten Seemannorcid logoAnna Syme avatar Anna SymeNiall Beard avatar Niall Beardorcid logoStéphanie Robin avatar Stéphanie RobinAva Hoffman avatar Ava Hoffmanorcid logoAlexandre Cormier avatar Alexandre CormierFrederick Tan avatar Frederick Tanorcid logoLaura Leroi avatar Laura Leroiorcid logoPaul Zierep avatar Paul Ziereporcid logoErwan Corre avatar Erwan Correorcid logoBjörn Grüning avatar Björn Grüningorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoSimon Gladman avatar Simon Gladmanorcid logoPeter van Heusden avatar Peter van Heusden

Funding

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

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