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 logoPaul Zierep avatar Paul Ziereporcid logoCristóbal Gallardo avatar Cristóbal GallardoElizabeth Humphries avatar Elizabeth HumphriesBazante Sanders avatar Bazante Sandersorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoMiaomiao Zhou avatar Miaomiao ZhouFrederick Tan avatar Frederick Tanorcid logoBérénice Batut avatar Bérénice Batutorcid logoSimon Gladman avatar Simon Gladmanorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton NekrutenkoJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoDeepti Varshney avatar Deepti VarshneyNathan Dunn avatar Nathan DunnYo Yehudi avatar Yo Yehudiorcid logoBjörn Grüning avatar Björn Grüningorcid logoErwan Corre avatar Erwan CorreCandace Savonen avatar Candace SavonenKatherine Cox avatar Katherine CoxNatalie Kucher avatar Natalie Kucherorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoTeresa Müller avatar Teresa MüllerAva Hoffman avatar Ava HoffmanDaniela Butano avatar Daniela Butanoorcid logoSaskia Hiltemann avatar Saskia HiltemannTorsten Seemann avatar Torsten Seemannorcid logoMateo Boudet avatar Mateo Boudetorcid logoLaura Leroi avatar Laura Leroiorcid logoAnna Syme avatar Anna Symeorcid logoAlexandre Cormier avatar Alexandre CormierRobert Meller avatar Robert MellerSimon Bray avatar Simon Brayorcid logoDelphine Lariviere avatar Delphine Lariviere

Funding

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