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

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 logoAnna Syme avatar Anna SymeNatalie Kucher avatar Natalie KucherCandace Savonen avatar Candace SavonenBazante Sanders avatar Bazante Sandersorcid logoSaskia Hiltemann avatar Saskia HiltemannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauDaniela Butano avatar Daniela Butanoorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTeresa Müller avatar Teresa Müllerorcid logoErwan Corre avatar Erwan Correorcid logoHelena Rasche avatar Helena Rascheorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMateo Boudet avatar Mateo BoudetSimon Bray avatar Simon Brayorcid logoBjörn Grüning avatar Björn Grüningorcid logoLaura Leroi avatar Laura LeroiJasper Ouwerkerk avatar Jasper OuwerkerkKatherine Cox avatar Katherine Coxorcid logoCristóbal Gallardo avatar Cristóbal GallardoTorsten Seemann avatar Torsten Seemannorcid logoBérénice Batut avatar Bérénice BatutElizabeth Humphries avatar Elizabeth HumphriesRobert Meller avatar Robert MellerNathan Dunn avatar Nathan Dunnorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoPaul Zierep avatar Paul ZierepYo Yehudi avatar Yo Yehudiorcid logoSimon Gladman avatar Simon GladmanAva Hoffman avatar Ava HoffmanFrederick Tan avatar Frederick Tanorcid logoAlexandre Cormier avatar Alexandre Cormier

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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ABRomics
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NHGRI ANVIL
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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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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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ELIXIR Europe
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Avans