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:

Natalie Kucher avatar Natalie Kucherorcid logoSaskia Hiltemann avatar Saskia HiltemannNathan Dunn avatar Nathan Dunnorcid logoBérénice Batut avatar Bérénice Batutorcid logoTeresa Müller avatar Teresa MüllerFrederick Tan avatar Frederick Tanorcid logoBjörn Grüning avatar Björn Grüningorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoHelena Rasche avatar Helena Rascheorcid logoLaura Leroi avatar Laura Leroiorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine LariviereBazante Sanders avatar Bazante Sandersorcid logoAlexandre Cormier avatar Alexandre CormierCandace Savonen avatar Candace SavonenSimon Bray avatar Simon BrayYo Yehudi avatar Yo Yehudiorcid logoMateo Boudet avatar Mateo BoudetNiall Beard avatar Niall BeardDaniela Butano avatar Daniela ButanoAva Hoffman avatar Ava HoffmanTorsten Seemann avatar Torsten Seemannorcid logoPaul Zierep avatar Paul Ziereporcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoMiaomiao Zhou avatar Miaomiao ZhouJasper Ouwerkerk avatar Jasper OuwerkerkRobert Meller avatar Robert Mellerorcid logoAnna Syme avatar Anna SymeAnton Nekrutenko avatar Anton NekrutenkoElizabeth Humphries avatar Elizabeth Humphriesorcid logoErwan Corre avatar Erwan Correorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoSimon Gladman avatar Simon Gladmanorcid logoMaria Doyle avatar Maria DoyleKatherine Cox avatar Katherine Cox

Funding

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

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Australian BioCommons
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NHGRI GDS Community Network
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ABRomics
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Melbourne Bioinformatics
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NHGRI ANVIL
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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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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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ELIXIR Europe
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Avans
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IFB