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 Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
nanopore assembly amr gmod jbrowse1 microgalaxy
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 apollo2
SARS-CoV-2 Viral Sample Alignment and Variant Visualization
covid19 gmod jbrowse1
Genome annotation with Funannotate
gmod eukaryote jbrowse1
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

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 apollo2
Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

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:

Torsten Seemann avatar Torsten SeemannKatherine Cox avatar Katherine CoxCandace Savonen avatar Candace SavonenYo Yehudi avatar Yo YehudiFrederick Tan avatar Frederick Tanorcid logoLaura Leroi avatar Laura Leroiorcid logoErwan Corre avatar Erwan CorreAnton Nekrutenko avatar Anton NekrutenkoNathan Dunn avatar Nathan DunnNatalie Kucher avatar Natalie Kucherorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoHelena Rasche avatar Helena Rascheorcid logoBérénice Batut avatar Bérénice Batutorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAnna Syme avatar Anna SymeAvans Hogeschool avatar Avans HogeschoolDaniela Butano avatar Daniela Butanoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoStéphanie Robin avatar Stéphanie RobinElizabeth Humphries avatar Elizabeth HumphriesAva Hoffman avatar Ava Hoffmanorcid logoSimon Gladman avatar Simon GladmanRobert Meller avatar Robert Mellerorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMateo Boudet avatar Mateo BoudetBazante Sanders avatar Bazante Sanders

Funding

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

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NHGRI GDS Community Network
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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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NHGRI ANVIL
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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.