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 logoTristan Reynolds avatar Tristan Reynoldsorcid logoMaria Doyle avatar Maria Doyleorcid logoMiaomiao Zhou avatar Miaomiao ZhouJasper Ouwerkerk avatar Jasper OuwerkerkNatalie Kucher avatar Natalie Kucherorcid logoCristóbal Gallardo avatar Cristóbal GallardoDaniela Butano avatar Daniela Butanoorcid logoErwan Corre avatar Erwan Correorcid logoRomane LIBOUBAN avatar Romane LIBOUBANFrederick Tan avatar Frederick Tanorcid logoNicola Soranzo avatar Nicola SoranzoNathan Dunn avatar Nathan Dunnorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoTeresa Müller avatar Teresa MüllerElizabeth Humphries avatar Elizabeth Humphriesorcid logoAlexandre Cormier avatar Alexandre CormierYo Yehudi avatar Yo Yehudiorcid logoAnna Syme avatar Anna SymeCandace Savonen avatar Candace Savonenorcid logoLaura Leroi avatar Laura Leroiorcid logoDeepti Varshney avatar Deepti VarshneyAnton Nekrutenko avatar Anton NekrutenkoRobert Meller avatar Robert Mellerorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoSaskia Hiltemann avatar Saskia HiltemannAva Hoffman avatar Ava Hoffmanorcid logoPeter van Heusden avatar Peter van HeusdenKatherine Cox avatar Katherine CoxTorsten Seemann avatar Torsten Seemannorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSimon Gladman avatar Simon GladmanBazante Sanders avatar Bazante SandersNiall Beard avatar Niall Beardorcid logoHelena Rasche avatar Helena RascheSimon Bray avatar Simon Brayorcid logoPaul Zierep avatar Paul Ziereporcid logoStéphanie Robin avatar Stéphanie Robinorcid logoBjörn Grüning avatar Björn Grüningorcid logoMateo Boudet avatar Mateo Boudet

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