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.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Material

JBrowse 1

Learn to use JBrowse v1 here.

Lesson Slides Hands-on Recordings Input dataset Workflows
Hands-on: Hands-on: Bacterial Genome Annotation
gmod illumina bacteria microgalaxy jbrowse1
Hands-on: Hands-on: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
nanopore assembly amr gmod jbrowse1 microgalaxy
Hands-on: Hands-on: Genome annotation with Prokka
gmod prokaryote microgalaxy jbrowse1
Hands-on: Hands-on: Genomic Data Visualisation with JBrowse
gmod jbrowse1
Hands-on: Hands-on: Identification of AMR genes in an assembled bacterial genome
gmod illumina amr one-health jbrowse1 microgalaxy
Hands-on: Hands-on: Making sense of a newly assembled genome
gmod prokaryote microgalaxy jbrowse1
Hands-on: Hands-on: Microbial Variant Calling
prokaryote microgalaxy gmod jbrowse1
Hands-on: Hands-on: Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 apollo2
Hands-on: Hands-on: SARS-CoV-2 Viral Sample Alignment and Variant Visualization
covid19 gmod jbrowse1
Hands-on: Hands-on: Genome annotation with Funannotate
gmod eukaryote jbrowse1
Hands-on: Hands-on: Genome annotation with Maker (short)
gmod eukaryote maker jbrowse1
Hands-on: Hands-on: Genome annotation with Maker
gmod eukaryote jbrowse1 maker
Hands-on: Hands-on: Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2

MAKER

Genome Annotation with MAKER.

Lesson Slides Hands-on Recordings Input dataset Workflows
Hands-on: Hands-on: Genome annotation with Maker (short)
gmod eukaryote maker jbrowse1
Hands-on: Hands-on: 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
Hands-on: Hands-on: 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
Hands-on: Hands-on: Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 apollo2
Hands-on: Hands-on: 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

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Katherine Cox avatar Katherine CoxAvans Hogeschool avatar Avans Hogeschoolorcid logoErwan Corre avatar Erwan Correorcid logoSaskia Hiltemann avatar Saskia HiltemannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSimon Gladman avatar Simon GladmanBazante Sanders avatar Bazante SandersNathan Dunn avatar Nathan DunnElizabeth Humphries avatar Elizabeth HumphriesDaniela Butano avatar Daniela Butanoorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoBérénice Batut avatar Bérénice Batutorcid logoMateo Boudet avatar Mateo BoudetNatalie Kucher avatar Natalie KucherAva Hoffman avatar Ava Hoffmanorcid logoLaura Leroi avatar Laura LeroiTorsten Seemann avatar Torsten Seemannorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoHelena Rasche avatar Helena Rascheorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnthony Bretaudeau avatar Anthony BretaudeauRobert Meller avatar Robert Mellerorcid logoAnna Syme avatar Anna SymeYo Yehudi avatar Yo Yehudiorcid logoAlexandre Cormier avatar Alexandre CormierFrederick Tan avatar Frederick TanCandace Savonen avatar Candace Savonen

Funders

This material was funded by:

ABRomics avatar ABRomicsNational Human Genome Research Institute Genomic Data Science Community Network avatar NHGRI GDS Community NetworkNational Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space avatar NHGRI ANVILEuroScienceGateway avatar EuroScienceGatewayGallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries