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 logoStéphanie Robin avatar Stéphanie Robinorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDeepti Varshney avatar Deepti VarshneyElizabeth Humphries avatar Elizabeth HumphriesAnton Nekrutenko avatar Anton NekrutenkoJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoTeresa Müller avatar Teresa MüllerCandace Savonen avatar Candace SavonenBazante Sanders avatar Bazante Sandersorcid logoRomane LIBOUBAN avatar Romane LIBOUBANNatalie Kucher avatar Natalie KucherNathan Dunn avatar Nathan DunnDaniela Butano avatar Daniela Butanoorcid logoAnna Syme avatar Anna Symeorcid logoBérénice Batut avatar Bérénice BatutRobert Meller avatar Robert Mellerorcid logoCristóbal Gallardo avatar Cristóbal GallardoFrederick Tan avatar Frederick TanYo Yehudi avatar Yo Yehudiorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoAlexandre Cormier avatar Alexandre CormierKatherine Cox avatar Katherine CoxNiall Beard avatar Niall Beardorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMaria Doyle avatar Maria Doyleorcid logoBjörn Grüning avatar Björn Grüningorcid logoMateo Boudet avatar Mateo Boudetorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoPaul Zierep avatar Paul ZierepTorsten Seemann avatar Torsten Seemannorcid logoHelena Rasche avatar Helena Rascheorcid logoSimon Gladman avatar Simon GladmanSimon Bray avatar Simon Brayorcid logoLaura Leroi avatar Laura LeroiAva Hoffman avatar Ava Hoffmanorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoErwan Corre avatar Erwan Corre

Funding

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

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