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:

Nathan Dunn avatar Nathan Dunnorcid logoBjörn Grüning avatar Björn Grüningorcid logoBérénice Batut avatar Bérénice Batutorcid logoLaura Leroi avatar Laura LeroiCandace Savonen avatar Candace SavonenRobert Meller avatar Robert MellerBazante Sanders avatar Bazante Sandersorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDeepti Varshney avatar Deepti VarshneyYo Yehudi avatar Yo Yehudiorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoPaul Zierep avatar Paul ZierepSimon Bray avatar Simon Brayorcid logoJonathan Kreplak avatar Jonathan KreplakAva Hoffman avatar Ava HoffmanTorsten Seemann avatar Torsten Seemannorcid logoCristóbal Gallardo avatar Cristóbal GallardoDaniela Butano avatar Daniela ButanoNatalie Kucher avatar Natalie KucherElizabeth Humphries avatar Elizabeth HumphriesFrederick Tan avatar Frederick Tanorcid logoSimon Gladman avatar Simon Gladmanorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoTeresa Müller avatar Teresa MüllerKatherine Cox avatar Katherine Coxorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAnna Syme avatar Anna SymeJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoErwan Corre avatar Erwan Corre

Funding

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