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 CorreRobert Meller avatar Robert Mellerorcid logoMaria Doyle avatar Maria Doyleorcid logoMiaomiao Zhou avatar Miaomiao ZhouNatalie Kucher avatar Natalie Kucherorcid logoAnna Syme avatar Anna Symeorcid logoCristóbal Gallardo avatar Cristóbal GallardoFrederick Tan avatar Frederick Tanorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAlexandre Cormier avatar Alexandre CormierTorsten Seemann avatar Torsten Seemannorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoMateo Boudet avatar Mateo Boudetorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-JacksonKatherine Cox avatar Katherine Coxorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnthony Bretaudeau avatar Anthony BretaudeauElizabeth Humphries avatar Elizabeth Humphriesorcid logoBérénice Batut avatar Bérénice Batutorcid logoTeresa Müller avatar Teresa Müllerorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoPaul Zierep avatar Paul ZierepDaniela Butano avatar Daniela ButanoJasper Ouwerkerk avatar Jasper OuwerkerkBazante Sanders avatar Bazante Sandersorcid logoTristan Reynolds avatar Tristan ReynoldsSimon Bray avatar Simon Brayorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoNicola Soranzo avatar Nicola SoranzoNathan Dunn avatar Nathan DunnYo Yehudi avatar Yo Yehudiorcid logoHelena Rasche avatar Helena RascheCandace Savonen avatar Candace Savonenorcid logoLaura Leroi avatar Laura LeroiNiall Beard avatar Niall Beardorcid logoSaskia Hiltemann avatar Saskia HiltemannAva Hoffman avatar Ava HoffmanAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSimon Gladman avatar Simon Gladman

Funding

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

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