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:

Nathan Dunn avatar Nathan DunnKatherine Cox avatar Katherine Coxorcid logoPaul Zierep avatar Paul ZierepTorsten Seemann avatar Torsten Seemannorcid logoMateo Boudet avatar Mateo BoudetElizabeth Humphries avatar Elizabeth HumphriesCandace Savonen avatar Candace Savonenorcid logoBjörn Grüning avatar Björn Grüningorcid logoDelphine Lariviere avatar Delphine LariviereFrederick Tan avatar Frederick Tanorcid logoJonathan Kreplak avatar Jonathan KreplakRobert Meller avatar Robert Mellerorcid logoHelena Rasche avatar Helena RascheYo Yehudi avatar Yo Yehudiorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoSaskia Hiltemann avatar Saskia HiltemannBazante Sanders avatar Bazante SandersDaniela Butano avatar Daniela ButanoAva Hoffman avatar Ava HoffmanAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoBérénice Batut avatar Bérénice Batutorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMaria Doyle avatar Maria Doyleorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoSimon Gladman avatar Simon GladmanNatalie Kucher avatar Natalie Kucherorcid logoTeresa Müller avatar Teresa Müllerorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoErwan Corre avatar Erwan Correorcid logoLaura Leroi avatar Laura Leroiorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoAnna Syme avatar Anna SymeNiall Beard avatar Niall Beardorcid logoDeepti Varshney avatar Deepti VarshneyJasper Ouwerkerk avatar Jasper OuwerkerkSimon Bray avatar Simon Brayorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Funding

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

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