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 LariviereAva Hoffman avatar Ava Hoffmanorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoTeresa Müller avatar Teresa Müllerorcid logoBérénice Batut avatar Bérénice BatutRobert Meller avatar Robert MellerNathan Dunn avatar Nathan Dunnorcid logoAnthony Bretaudeau avatar Anthony BretaudeauNiall Beard avatar Niall Beardorcid logoRomane LIBOUBAN avatar Romane LIBOUBANElizabeth Humphries avatar Elizabeth Humphriesorcid logoMaria Doyle avatar Maria Doyleorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoTristan Reynolds avatar Tristan ReynoldsJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoAnna Syme avatar Anna Symeorcid logoMateo Boudet avatar Mateo Boudetorcid logoHelena Rasche avatar Helena RascheFrederick Tan avatar Frederick Tanorcid logoPaul Zierep avatar Paul ZierepBazante Sanders avatar Bazante SandersSimon Bray avatar Simon Brayorcid logoBjörn Grüning avatar Björn GrüningDaniela Butano avatar Daniela Butanoorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoAlexandre Cormier avatar Alexandre CormierTorsten Seemann avatar Torsten Seemannorcid logoMiaomiao Zhou avatar Miaomiao ZhouKatherine Cox avatar Katherine Coxorcid logoLaura Leroi avatar Laura LeroiCandace Savonen avatar Candace Savonenorcid logoErwan Corre avatar Erwan Correorcid logoJonathan Kreplak avatar Jonathan KreplakAnton Nekrutenko avatar Anton NekrutenkoYo Yehudi avatar Yo Yehudiorcid logoSimon Gladman avatar Simon GladmanNatalie Kucher avatar Natalie Kucherorcid logoStéphanie Robin avatar Stéphanie Robin

Funding

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

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