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 (slides) and tutorial (tutorial) buttons below.

JBrowse 1

Learn to use JBrowse v1 here.

Lesson Slides Hands-on Recordings Input dataset Workflows
Bacterial Genome Annotation
Genome annotation with Prokka
Genomic Data Visualisation with JBrowse
Identification of AMR genes in an assembled bacterial genome
Making sense of a newly assembled genome
Microbial Variant Calling
Refining Genome Annotations with Apollo (prokaryotes)
SARS-CoV-2 Viral Sample Alignment and Variant Visualization
Genome annotation with Funannotate
Genome annotation with Maker (short)
Genome annotation with Maker
Refining Genome Annotations with Apollo (eukaryotes)

MAKER

Genome Annotation with MAKER.

Lesson Slides Hands-on Recordings Input dataset Workflows
Genome annotation with Maker (short)
Genome annotation with 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

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)
Refining Genome Annotations with Apollo (eukaryotes)

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:

orcid logoSimon Gladman avatar Simon Gladmanorcid logoErwan Corre avatar Erwan CorreNathan Dunn avatar Nathan Dunnorcid logoTeresa Müller avatar Teresa Müllerorcid logoDelphine Lariviere avatar Delphine LariviereNatalie Kucher avatar Natalie KucherTorsten Seemann avatar Torsten Seemannorcid logoDeepti Varshney avatar Deepti VarshneyFrederick Tan avatar Frederick TanAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMateo Boudet avatar Mateo Boudetorcid logoHelena Rasche avatar Helena RascheSimon Bray avatar Simon Brayorcid logoLaura Leroi avatar Laura LeroiBazante Sanders avatar Bazante SandersElizabeth Humphries avatar Elizabeth Humphriesorcid logoBérénice Batut avatar Bérénice Batutorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAlexandre Cormier avatar Alexandre CormierDaniela Butano avatar Daniela Butanoorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoAnna Syme avatar Anna Symeorcid logoBjörn Grüning avatar Björn GrüningRobert Meller avatar Robert MellerAva Hoffman avatar Ava Hoffmanorcid logoPaul Zierep avatar Paul ZierepCandace Savonen avatar Candace Savonenorcid logoAnthony Bretaudeau avatar Anthony BretaudeauKatherine Cox avatar Katherine CoxYo Yehudi avatar Yo Yehudiorcid logoStéphanie Robin avatar Stéphanie RobinJasper Ouwerkerk avatar Jasper Ouwerkerk

Funding

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