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

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:

Katherine Cox avatar Katherine Coxorcid logoMaria Doyle avatar Maria DoyleAnton Nekrutenko avatar Anton Nekrutenkoorcid logoTristan Reynolds avatar Tristan ReynoldsNathan Dunn avatar Nathan DunnJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoPaul Zierep avatar Paul Ziereporcid logoTeresa Müller avatar Teresa MüllerCandace Savonen avatar Candace Savonenorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoBérénice Batut avatar Bérénice BatutDaniela Butano avatar Daniela ButanoElizabeth Humphries avatar Elizabeth Humphriesorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoBjörn Grüning avatar Björn GrüningBazante Sanders avatar Bazante Sandersorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoJonathan Kreplak avatar Jonathan KreplakRobert Meller avatar Robert MellerYo Yehudi avatar Yo Yehudiorcid logoAnna Syme avatar Anna SymeNiall Beard avatar Niall Beardorcid logoSimon Gladman avatar Simon Gladmanorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoMateo Boudet avatar Mateo Boudetorcid logoLaura Leroi avatar Laura Leroiorcid logoStéphanie Robin avatar Stéphanie RobinFrederick Tan avatar Frederick Tanorcid logoErwan Corre avatar Erwan Correorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoDeepti Varshney avatar Deepti VarshneySimon Bray avatar Simon Brayorcid logoHelena Rasche avatar Helena RascheTorsten Seemann avatar Torsten SeemannAva Hoffman avatar Ava HoffmanNatalie Kucher avatar Natalie Kucher

Funding

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

Logo
Avans
Logo
ABRomics
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.
Logo
NHGRI GDS Community Network
Logo
The University of Melbourne
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
Melbourne Bioinformatics
Logo
Australian BioCommons