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
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
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

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 (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2 biodiversity
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 biodiversity apollo2

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 logoErwan Corre avatar Erwan Correorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoSimon Gladman avatar Simon GladmanJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoDeepti Varshney avatar Deepti VarshneyYo Yehudi avatar Yo Yehudiorcid logoBérénice Batut avatar Bérénice BatutCandace Savonen avatar Candace SavonenElizabeth Humphries avatar Elizabeth Humphriesorcid logoLaura Leroi avatar Laura Leroiorcid logoMiaomiao Zhou avatar Miaomiao ZhouTorsten Seemann avatar Torsten Seemannorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNicola Soranzo avatar Nicola SoranzoBazante Sanders avatar Bazante SandersKatherine Cox avatar Katherine Coxorcid logoAnna Syme avatar Anna Symeorcid logoPaul Zierep avatar Paul ZierepRobert Meller avatar Robert Mellerorcid logoTristan Reynolds avatar Tristan ReynoldsNatalie Kucher avatar Natalie Kucherorcid logoBjörn Grüning avatar Björn GrüningNiall Beard avatar Niall BeardSimon Bray avatar Simon Brayorcid logoMateo Boudet avatar Mateo Boudetorcid logoTeresa Müller avatar Teresa MüllerNathan Dunn avatar Nathan Dunnorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMaria Doyle avatar Maria Doyleorcid logoStéphanie Robin avatar Stéphanie RobinFrederick Tan avatar Frederick Tanorcid logoHelena Rasche avatar Helena RascheAva Hoffman avatar Ava Hoffmanorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoRomane LIBOUBAN avatar Romane LIBOUBANDaniela Butano avatar Daniela Butanoorcid logoAlexandre Cormier avatar Alexandre CormierAnton Nekrutenko avatar Anton Nekrutenkoorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Funding

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

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