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 logoTristan Reynolds avatar Tristan ReynoldsAva Hoffman avatar Ava Hoffmanorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoErwan Corre avatar Erwan Correorcid logoLaura Leroi avatar Laura Leroiorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMaria Doyle avatar Maria Doyleorcid logoNicola Soranzo avatar Nicola SoranzoAnton Nekrutenko avatar Anton NekrutenkoJasper Ouwerkerk avatar Jasper OuwerkerkTorsten Seemann avatar Torsten Seemannorcid logoDelphine Lariviere avatar Delphine LariviereYo Yehudi avatar Yo YehudiElizabeth Humphries avatar Elizabeth HumphriesNiall Beard avatar Niall Beardorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoBérénice Batut avatar Bérénice Batutorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnna Syme avatar Anna Symeorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoStéphanie Robin avatar Stéphanie RobinNathan Dunn avatar Nathan Dunnorcid logoSimon Gladman avatar Simon GladmanRobert Meller avatar Robert Mellerorcid logoPaul Zierep avatar Paul ZierepSimon Bray avatar Simon BrayCandace Savonen avatar Candace SavonenBazante Sanders avatar Bazante Sandersorcid logoHelena Rasche avatar Helena Rascheorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoCristóbal Gallardo avatar Cristóbal GallardoFrederick Tan avatar Frederick TanKatherine Cox avatar Katherine Coxorcid logoSaskia Hiltemann avatar Saskia HiltemannDaniela Butano avatar Daniela Butanoorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoMateo Boudet avatar Mateo Boudetorcid logoTeresa Müller avatar Teresa MüllerNatalie Kucher avatar Natalie Kucherorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Funding

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

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