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 Reynoldsorcid logoLaura Leroi avatar Laura Leroiorcid logoBjörn Grüning avatar Björn GrüningNathan Dunn avatar Nathan Dunnorcid logoAnna Syme avatar Anna Symeorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMaria Doyle avatar Maria DoyleKatherine Cox avatar Katherine CoxFrederick Tan avatar Frederick TanRobert Meller avatar Robert MellerNatalie Kucher avatar Natalie Kucherorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMateo Boudet avatar Mateo BoudetAnton Nekrutenko avatar Anton Nekrutenkoorcid logoPaul Zierep avatar Paul Ziereporcid logoHelena Rasche avatar Helena Rascheorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-JacksonBazante Sanders avatar Bazante Sandersorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNicola Soranzo avatar Nicola SoranzoSimon Bray avatar Simon Brayorcid logoSimon Gladman avatar Simon Gladmanorcid logoBérénice Batut avatar Bérénice BatutJasper Ouwerkerk avatar Jasper OuwerkerkNiall Beard avatar Niall BeardAva Hoffman avatar Ava Hoffmanorcid logoDeepti Varshney avatar Deepti VarshneyTorsten Seemann avatar Torsten Seemannorcid logoErwan Corre avatar Erwan CorreElizabeth Humphries avatar Elizabeth HumphriesYo Yehudi avatar Yo YehudiCandace Savonen avatar Candace Savonenorcid logoTeresa Müller avatar Teresa Müllerorcid logoAlexandre Cormier avatar Alexandre CormierDaniela Butano avatar Daniela Butano

Funding

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

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