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:

Gildas Le Corguillé avatar Gildas Le CorguilléTorsten Seemann avatar Torsten Seemannorcid logoAnthony Bretaudeau avatar Anthony BretaudeauCandace Savonen avatar Candace Savonenorcid logoLaura Leroi avatar Laura LeroiRobert Meller avatar Robert Mellerorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoPeter van Heusden avatar Peter van HeusdenKatherine Cox avatar Katherine CoxDaniela Butano avatar Daniela Butanoorcid logoBjörn Grüning avatar Björn Grüningorcid logoMaria Doyle avatar Maria Doyleorcid logoCristóbal Gallardo avatar Cristóbal GallardoElizabeth Humphries avatar Elizabeth HumphriesAva Hoffman avatar Ava Hoffmanorcid logoAnna Syme avatar Anna SymeAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoBérénice Batut avatar Bérénice Batutorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoMiaomiao Zhou avatar Miaomiao ZhouYo Yehudi avatar Yo YehudiFrederick Tan avatar Frederick Tanorcid logoMateo Boudet avatar Mateo Boudetorcid logoTeresa Müller avatar Teresa MüllerSimon Bray avatar Simon Brayorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoNicola Soranzo avatar Nicola SoranzoNathan Dunn avatar Nathan DunnNatalie Kucher avatar Natalie Kucherorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoHelena Rasche avatar Helena Rascheorcid logoSimon Gladman avatar Simon Gladmanorcid logoErwan Corre avatar Erwan Correorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoPaul Zierep avatar Paul ZierepNiall Beard avatar Niall Beardorcid logoDeepti Varshney avatar Deepti VarshneyJasper Ouwerkerk avatar Jasper OuwerkerkBazante Sanders avatar Bazante Sandersorcid logoRomane LIBOUBAN avatar Romane LIBOUBAN

Funding

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

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