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:

Jasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoAlexandre Cormier avatar Alexandre CormierSimon Bray avatar Simon Brayorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoBérénice Batut avatar Bérénice Batutorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoMateo Boudet avatar Mateo Boudetorcid logoErwan Corre avatar Erwan Correorcid logoAnthony Bretaudeau avatar Anthony BretaudeauKatherine Cox avatar Katherine CoxDaniela Butano avatar Daniela Butanoorcid logoLaura Leroi avatar Laura LeroiAnton Nekrutenko avatar Anton NekrutenkoYo Yehudi avatar Yo Yehudiorcid logoAnna Syme avatar Anna SymeFrederick Tan avatar Frederick Tanorcid logoHelena Rasche avatar Helena Rascheorcid logoBjörn Grüning avatar Björn Grüningorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNicola Soranzo avatar Nicola SoranzoNatalie Kucher avatar Natalie Kucherorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoMiaomiao Zhou avatar Miaomiao ZhouNathan Dunn avatar Nathan DunnTorsten Seemann avatar Torsten Seemannorcid logoPaul Zierep avatar Paul ZierepRobert Meller avatar Robert Mellerorcid logoTeresa Müller avatar Teresa MüllerCandace Savonen avatar Candace SavonenNiall Beard avatar Niall Beardorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoSimon Gladman avatar Simon Gladmanorcid logoPeter van Heusden avatar Peter van HeusdenAva Hoffman avatar Ava Hoffmanorcid logoJonathan Kreplak avatar Jonathan KreplakElizabeth Humphries avatar Elizabeth Humphriesorcid logoMaria Doyle avatar Maria Doyleorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoCristóbal Gallardo avatar Cristóbal GallardoBazante Sanders avatar Bazante Sanders

Funding

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

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