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 Rasche orcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Contributors

This material was contributed to by:

orcid logoMaria Doyle avatar Maria Doyle Torsten Seemann avatar Torsten Seemann Niall Beard avatar Niall Beard Katherine Cox avatar Katherine Cox orcid logoDelphine Lariviere avatar Delphine Lariviere orcid logoBjörn Grüning avatar Björn Grüning Frederick Tan avatar Frederick Tan orcid logoNicola Soranzo avatar Nicola Soranzo orcid logoAnna Syme avatar Anna Syme Simon Bray avatar Simon Bray Yo Yehudi avatar Yo Yehudi Jasper Ouwerkerk avatar Jasper Ouwerkerk Elizabeth Humphries avatar Elizabeth Humphries orcid logoJonathan Kreplak avatar Jonathan Kreplak orcid logoCristóbal Gallardo avatar Cristóbal Gallardo orcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jackson orcid logoPaul Zierep avatar Paul Zierep Ava Hoffman avatar Ava Hoffman orcid logoMateo Boudet avatar Mateo Boudet orcid logoStéphanie Robin avatar Stéphanie Robin orcid logoMiaomiao Zhou avatar Miaomiao Zhou Anton Nekrutenko avatar Anton Nekrutenko Deepti Varshney avatar Deepti Varshney Natalie Kucher avatar Natalie Kucher orcid logoErwan Corre avatar Erwan Corre orcid logoSaskia Hiltemann avatar Saskia Hiltemann Daniela Butano avatar Daniela Butano Candace Savonen avatar Candace Savonen Robert Meller avatar Robert Meller orcid logoAnthony Bretaudeau avatar Anthony Bretaudeau Teresa Müller avatar Teresa Müller Gildas Le Corguillé avatar Gildas Le Corguillé orcid logoAlexandre Cormier avatar Alexandre Cormier orcid logoHelena Rasche avatar Helena Rasche orcid logoLaura Leroi avatar Laura Leroi Nathan Dunn avatar Nathan Dunn orcid logoBérénice Batut avatar Bérénice Batut Bazante Sanders avatar Bazante Sanders orcid logoSimon Gladman avatar Simon Gladman orcid logoPeter van Heusden avatar Peter van Heusden

Funding

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

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ELIXIR Europe
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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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Avans
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IFB
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NHGRI GDS Community Network
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ABRomics
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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.