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 logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoStéphanie Robin avatar Stéphanie RobinTorsten Seemann avatar Torsten SeemannNiall Beard avatar Niall BeardSimon Bray avatar Simon BrayYo Yehudi avatar Yo YehudiKatherine Cox avatar Katherine Coxorcid logoMateo Boudet avatar Mateo BoudetNatalie Kucher avatar Natalie Kucherorcid logoBjörn Grüning avatar Björn Grüningorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoSimon Gladman avatar Simon Gladmanorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoErwan Corre avatar Erwan Correorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoTeresa Müller avatar Teresa Müllerorcid logoLaura Leroi avatar Laura LeroiBazante Sanders avatar Bazante Sandersorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnna Syme avatar Anna Symeorcid logoAlexandre Cormier avatar Alexandre CormierCandace Savonen avatar Candace Savonenorcid logoPaul Zierep avatar Paul ZierepRobert Meller avatar Robert Mellerorcid logoMiaomiao Zhou avatar Miaomiao ZhouElizabeth Humphries avatar Elizabeth Humphriesorcid logoHelena Rasche avatar Helena Rascheorcid logoMaria Doyle avatar Maria DoyleNathan Dunn avatar Nathan DunnAnton Nekrutenko avatar Anton Nekrutenkoorcid logoJonathan Kreplak avatar Jonathan KreplakDaniela Butano avatar Daniela ButanoJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoTristan Reynolds avatar Tristan ReynoldsFrederick Tan avatar Frederick TanAva Hoffman avatar Ava Hoffman

Funding

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

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