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:

Candace Savonen avatar Candace SavonenSimon Bray avatar Simon BrayElizabeth Humphries avatar Elizabeth Humphriesorcid logoErwan Corre avatar Erwan CorreNatalie Kucher avatar Natalie Kucherorcid logoMateo Boudet avatar Mateo Boudetorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoBjörn Grüning avatar Björn Grüningorcid logoBérénice Batut avatar Bérénice BatutFrederick Tan avatar Frederick Tanorcid logoSimon Gladman avatar Simon GladmanRobert Meller avatar Robert Mellerorcid logoDelphine Lariviere avatar Delphine LariviereNathan Dunn avatar Nathan Dunnorcid logoPaul Zierep avatar Paul ZierepTorsten Seemann avatar Torsten Seemannorcid logoTeresa Müller avatar Teresa MüllerAva Hoffman avatar Ava HoffmanDaniela Butano avatar Daniela ButanoKatherine Cox avatar Katherine CoxYo Yehudi avatar Yo Yehudiorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnna Syme avatar Anna Symeorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoLaura Leroi avatar Laura LeroiBazante Sanders avatar Bazante Sanders

Funding

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

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NHGRI ANVIL
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Avans
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IFB
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ELIXIR Europe
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ABRomics
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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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NHGRI GDS Community Network