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
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
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

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 (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2 biodiversity
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 biodiversity apollo2

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
Genomic Data Visualisation with JBrowse2
gmod jbrowse2

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 logoMateo Boudet avatar Mateo Boudetorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoPaul Zierep avatar Paul Ziereporcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMiaomiao Zhou avatar Miaomiao ZhouCandace Savonen avatar Candace Savonenorcid logoBjörn Grüning avatar Björn Grüningorcid logoTristan Reynolds avatar Tristan ReynoldsRobert Meller avatar Robert Mellerorcid logoJonathan Kreplak avatar Jonathan KreplakAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSimon Gladman avatar Simon GladmanAva Hoffman avatar Ava Hoffmanorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMaria Doyle avatar Maria Doyleorcid logoHelena Rasche avatar Helena Rascheorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-JacksonNatalie Kucher avatar Natalie KucherDaniela Butano avatar Daniela Butanoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnna Syme avatar Anna SymeTorsten Seemann avatar Torsten Seemannorcid logoTeresa Müller avatar Teresa MüllerFrederick Tan avatar Frederick Tanorcid logoAlexandre Cormier avatar Alexandre CormierElizabeth Humphries avatar Elizabeth Humphriesorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoLaura Leroi avatar Laura LeroiJasper Ouwerkerk avatar Jasper OuwerkerkSimon Bray avatar Simon BrayKatherine Cox avatar Katherine Coxorcid logoBérénice Batut avatar Bérénice BatutNiall Beard avatar Niall Beardorcid logoAnthony Bretaudeau avatar Anthony BretaudeauNathan Dunn avatar Nathan Dunnorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoRomane LIBOUBAN avatar Romane LIBOUBANYo Yehudi avatar Yo Yehudiorcid logoErwan Corre avatar Erwan CorreBazante Sanders avatar Bazante Sanders

Funding

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

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