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 apollo2
SARS-CoV-2 Viral Sample Alignment and Variant Visualization
covid19 gmod jbrowse1
Genome annotation with Funannotate
gmod eukaryote jbrowse1
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

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 apollo2
Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2

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 logoSimon Gladman avatar Simon GladmanKatherine Cox avatar Katherine CoxElizabeth Humphries avatar Elizabeth Humphriesorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauAva Hoffman avatar Ava Hoffmanorcid logoErwan Corre avatar Erwan CorreCandace Savonen avatar Candace SavonenNathan Dunn avatar Nathan DunnNatalie Kucher avatar Natalie Kucherorcid logoAlexandre Cormier avatar Alexandre CormierTeresa Müller avatar Teresa MüllerAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHelena Rasche avatar Helena Rascheorcid logoAnna Syme avatar Anna Symeorcid logoMiaomiao Zhou avatar Miaomiao ZhouTorsten Seemann avatar Torsten SeemannSimon Bray avatar Simon Brayorcid logoMateo Boudet avatar Mateo Boudetorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoPaul Zierep avatar Paul ZierepDaniela Butano avatar Daniela ButanoYo Yehudi avatar Yo YehudiRobert Meller avatar Robert MellerBazante Sanders avatar Bazante SandersDeepti Varshney avatar Deepti Varshneyorcid logoBjörn Grüning avatar Björn GrüningJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoBérénice Batut avatar Bérénice Batutorcid logoLaura Leroi avatar Laura LeroiFrederick Tan avatar Frederick Tan

Funding

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

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ABRomics
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NHGRI ANVIL
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Avans
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ELIXIR Europe
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IFB
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NHGRI GDS Community Network
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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.