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:

Candace Savonen avatar Candace Savonenorcid logoMateo Boudet avatar Mateo Boudetorcid logoJonathan Kreplak avatar Jonathan KreplakAva Hoffman avatar Ava HoffmanDaniela Butano avatar Daniela Butanoorcid logoTeresa Müller avatar Teresa MüllerYo Yehudi avatar Yo Yehudiorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoLaura Leroi avatar Laura Leroiorcid logoPaul Zierep avatar Paul ZierepNatalie Kucher avatar Natalie KucherKatherine Cox avatar Katherine Coxorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJasper Ouwerkerk avatar Jasper OuwerkerkRobert Meller avatar Robert Mellerorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoErwan Corre avatar Erwan CorreSimon Bray avatar Simon Brayorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSimon Gladman avatar Simon GladmanAnton Nekrutenko avatar Anton NekrutenkoElizabeth Humphries avatar Elizabeth HumphriesBazante Sanders avatar Bazante SandersNathan Dunn avatar Nathan Dunnorcid logoAnna Syme avatar Anna Symeorcid logoBjörn Grüning avatar Björn GrüningFrederick Tan avatar Frederick Tanorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia HiltemannTorsten Seemann avatar Torsten Seemann

Funding

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