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 logoCristóbal Gallardo avatar Cristóbal GallardoBazante Sanders avatar Bazante SandersJasper Ouwerkerk avatar Jasper OuwerkerkNiall Beard avatar Niall BeardYo Yehudi avatar Yo YehudiAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBjörn Grüning avatar Björn Grüningorcid logoMaria Doyle avatar Maria DoyleRobert Meller avatar Robert Mellerorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMateo Boudet avatar Mateo Boudetorcid logoSimon Gladman avatar Simon GladmanNatalie Kucher avatar Natalie Kucherorcid logoHelena Rasche avatar Helena Rascheorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoTeresa Müller avatar Teresa MüllerDaniela Butano avatar Daniela Butanoorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoPaul Zierep avatar Paul ZierepKatherine Cox avatar Katherine CoxNathan Dunn avatar Nathan DunnCandace Savonen avatar Candace SavonenSimon Bray avatar Simon Brayorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoLaura Leroi avatar Laura Leroiorcid logoAnna Syme avatar Anna Symeorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoBérénice Batut avatar Bérénice Batutorcid logoTristan Reynolds avatar Tristan ReynoldsAva Hoffman avatar Ava Hoffmanorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDeepti Varshney avatar Deepti VarshneyTorsten Seemann avatar Torsten Seemannorcid logoStéphanie Robin avatar Stéphanie RobinElizabeth Humphries avatar Elizabeth HumphriesFrederick Tan avatar Frederick Tanorcid logoErwan Corre avatar Erwan Correorcid logoSaskia Hiltemann avatar Saskia Hiltemann

Funding

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

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