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 logoDeepti Varshney avatar Deepti Varshneyorcid logoDelphine Lariviere avatar Delphine LariviereYo Yehudi avatar Yo Yehudiorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoTeresa Müller avatar Teresa Müllerorcid logoJonathan Kreplak avatar Jonathan KreplakAva Hoffman avatar Ava Hoffmanorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBérénice Batut avatar Bérénice Batutorcid logoBjörn Grüning avatar Björn Grüningorcid logoPaul Zierep avatar Paul Ziereporcid logoAnna Syme avatar Anna SymeJasper Ouwerkerk avatar Jasper OuwerkerkNiall Beard avatar Niall BeardDaniela Butano avatar Daniela Butanoorcid logoSimon Gladman avatar Simon Gladmanorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMateo Boudet avatar Mateo Boudetorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSaskia Hiltemann avatar Saskia HiltemannNathan Dunn avatar Nathan Dunnorcid logoLaura Leroi avatar Laura LeroiElizabeth Humphries avatar Elizabeth HumphriesFrederick Tan avatar Frederick Tanorcid logoPeter van Heusden avatar Peter van HeusdenRobert Meller avatar Robert MellerAnton Nekrutenko avatar Anton NekrutenkoNatalie Kucher avatar Natalie KucherSimon Bray avatar Simon Brayorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoErwan Corre avatar Erwan Correorcid logoMaria Doyle avatar Maria DoyleTorsten Seemann avatar Torsten SeemannBazante Sanders avatar Bazante Sandersorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoHelena Rasche avatar Helena Rascheorcid logoTristan Reynolds avatar Tristan ReynoldsCandace Savonen avatar Candace Savonenorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-JacksonKatherine Cox avatar Katherine Cox

Funding

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

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