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 logoTeresa Müller avatar Teresa MüllerElizabeth Humphries avatar Elizabeth HumphriesNatalie Kucher avatar Natalie Kucherorcid logoMateo Boudet avatar Mateo BoudetFrederick Tan avatar Frederick Tanorcid logoPaul Zierep avatar Paul ZierepYo Yehudi avatar Yo Yehudiorcid logoJonathan Kreplak avatar Jonathan KreplakNathan Dunn avatar Nathan Dunnorcid logoSimon Gladman avatar Simon Gladmanorcid logoLaura Leroi avatar Laura Leroiorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoBjörn Grüning avatar Björn GrüningTorsten Seemann avatar Torsten Seemannorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoCristóbal Gallardo avatar Cristóbal GallardoKatherine Cox avatar Katherine CoxBazante Sanders avatar Bazante Sandersorcid logoErwan Corre avatar Erwan CorreRobert Meller avatar Robert MellerSimon Bray avatar Simon Brayorcid logoDelphine Lariviere avatar Delphine LariviereCandace Savonen avatar Candace Savonenorcid logoSaskia Hiltemann avatar Saskia HiltemannDaniela Butano avatar Daniela Butanoorcid logoBérénice Batut avatar Bérénice Batutorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoHelena Rasche avatar Helena RascheAva Hoffman avatar Ava Hoffmanorcid logoAnna Syme avatar Anna SymeAnton Nekrutenko avatar Anton NekrutenkoJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoStéphanie Robin avatar Stéphanie Robin

Funding

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