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:

Natalie Kucher avatar Natalie Kucherorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMiaomiao Zhou avatar Miaomiao ZhouBazante Sanders avatar Bazante SandersNathan Dunn avatar Nathan DunnElizabeth Humphries avatar Elizabeth Humphriesorcid logoSaskia Hiltemann avatar Saskia HiltemannNiall Beard avatar Niall Beardorcid logoErwan Corre avatar Erwan Correorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoBjörn Grüning avatar Björn Grüningorcid logoBérénice Batut avatar Bérénice Batutorcid logoDelphine Lariviere avatar Delphine LariviereCandace Savonen avatar Candace Savonenorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDeepti Varshney avatar Deepti VarshneyRobert Meller avatar Robert MellerJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoAnna Syme avatar Anna Symeorcid logoPaul Zierep avatar Paul Ziereporcid logoTeresa Müller avatar Teresa Müllerorcid logoRomane LIBOUBAN avatar Romane LIBOUBANFrederick Tan avatar Frederick Tanorcid logoLaura Leroi avatar Laura Leroiorcid logoMaria Doyle avatar Maria DoyleYo Yehudi avatar Yo YehudiTorsten Seemann avatar Torsten SeemannDaniela Butano avatar Daniela Butanoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauSimon Bray avatar Simon Brayorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoSimon Gladman avatar Simon Gladmanorcid logoTristan Reynolds avatar Tristan ReynoldsKatherine Cox avatar Katherine Coxorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoNicola Soranzo avatar Nicola SoranzoAva Hoffman avatar Ava Hoffmanorcid logoMateo Boudet avatar Mateo Boudet

Funding

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

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