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

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 logoAnna Syme avatar Anna SymeSimon Bray avatar Simon BrayJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoTeresa Müller avatar Teresa Müllerorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-JacksonYo Yehudi avatar Yo YehudiNatalie Kucher avatar Natalie Kucherorcid logoMateo Boudet avatar Mateo BoudetFrederick Tan avatar Frederick Tanorcid logoBjörn Grüning avatar Björn Grüningorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSaskia Hiltemann avatar Saskia HiltemannElizabeth Humphries avatar Elizabeth Humphriesorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoDelphine Lariviere avatar Delphine LariviereNiall Beard avatar Niall Beardorcid logoJonathan Kreplak avatar Jonathan KreplakRobert Meller avatar Robert Mellerorcid logoMiaomiao Zhou avatar Miaomiao ZhouKatherine Cox avatar Katherine CoxCandace Savonen avatar Candace Savonenorcid logoPaul Zierep avatar Paul ZierepAva Hoffman avatar Ava HoffmanNathan Dunn avatar Nathan Dunnorcid logoSimon Gladman avatar Simon GladmanDaniela Butano avatar Daniela Butanoorcid logoCristóbal Gallardo avatar Cristóbal GallardoTorsten Seemann avatar Torsten SeemannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMaria Doyle avatar Maria Doyleorcid logoHelena Rasche avatar Helena Rascheorcid logoBérénice Batut avatar Bérénice Batutorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoLaura Leroi avatar Laura LeroiBazante Sanders avatar Bazante Sandersorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoErwan Corre avatar Erwan Corre

Funding

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

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