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:

Anton Nekrutenko avatar Anton Nekrutenkoorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoTeresa Müller avatar Teresa MüllerNiall Beard avatar Niall Beardorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNicola Soranzo avatar Nicola SoranzoAva Hoffman avatar Ava HoffmanJasper Ouwerkerk avatar Jasper OuwerkerkTorsten Seemann avatar Torsten Seemannorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoStéphanie Robin avatar Stéphanie RobinElizabeth Humphries avatar Elizabeth HumphriesNathan Dunn avatar Nathan DunnDaniela Butano avatar Daniela Butanoorcid logoCristóbal Gallardo avatar Cristóbal GallardoYo Yehudi avatar Yo Yehudiorcid logoHelena Rasche avatar Helena Rascheorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-JacksonFrederick Tan avatar Frederick Tanorcid logoBjörn Grüning avatar Björn GrüningBazante Sanders avatar Bazante Sandersorcid logoAnna Syme avatar Anna Symeorcid logoDelphine Lariviere avatar Delphine LariviereKatherine Cox avatar Katherine Coxorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoErwan Corre avatar Erwan Correorcid logoTristan Reynolds avatar Tristan ReynoldsCandace Savonen avatar Candace Savonenorcid logoMateo Boudet avatar Mateo Boudetorcid logoLaura Leroi avatar Laura LeroiSimon Bray avatar Simon Brayorcid logoPaul Zierep avatar Paul ZierepRobert Meller avatar Robert MellerNatalie Kucher avatar Natalie Kucherorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSimon Gladman avatar Simon Gladmanorcid logoMaria Doyle avatar Maria Doyleorcid logoJonathan Kreplak avatar Jonathan Kreplak

Funding

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

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