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.

For any question or discussions related to this topic, or to connect with others in the community, please visit the community chat:

  Community Matrix Chat

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

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:

Bazante Sanders avatar Bazante Sandersorcid logoMateo Boudet avatar Mateo Boudetorcid logoStéphanie Robin avatar Stéphanie RobinSimon Bray avatar Simon Brayorcid logoMaria Doyle avatar Maria DoyleKatherine Cox avatar Katherine Coxorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-JacksonTorsten Seemann avatar Torsten Seemannorcid logoErwan Corre avatar Erwan CorreJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoSimon Gladman avatar Simon Gladmanorcid logoTeresa Müller avatar Teresa Müllerorcid logoPaul Zierep avatar Paul ZierepDaniela Butano avatar Daniela ButanoAva Hoffman avatar Ava Hoffmanorcid logoAnthony Bretaudeau avatar Anthony BretaudeauCandace Savonen avatar Candace Savonenorcid logoHelena Rasche avatar Helena Rascheorcid logoBjörn Grüning avatar Björn GrüningElizabeth Humphries avatar Elizabeth HumphriesNiall Beard avatar Niall BeardFrederick Tan avatar Frederick Tanorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoSaskia Hiltemann avatar Saskia HiltemannYo Yehudi avatar Yo Yehudiorcid logoLaura Leroi avatar Laura Leroiorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnna Syme avatar Anna Symeorcid logoMiaomiao Zhou avatar Miaomiao ZhouRobert Meller avatar Robert MellerNathan Dunn avatar Nathan Dunnorcid logoNicola Soranzo avatar Nicola SoranzoNatalie Kucher avatar Natalie Kucherorcid logoAlexandre Cormier avatar Alexandre CormierAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBérénice Batut avatar Bérénice Batutorcid logoPeter van Heusden avatar Peter van Heusden

Funding

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

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