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:

Katherine Cox avatar Katherine Coxorcid logoHelena Rasche avatar Helena Rascheorcid logoStéphanie Robin avatar Stéphanie RobinDaniela Butano avatar Daniela Butanoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoErwan Corre avatar Erwan Correorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoJonathan Kreplak avatar Jonathan KreplakSimon Bray avatar Simon BrayNatalie Kucher avatar Natalie KucherAnton Nekrutenko avatar Anton Nekrutenkoorcid logoPaul Zierep avatar Paul ZierepYo Yehudi avatar Yo YehudiFrederick Tan avatar Frederick TanBazante Sanders avatar Bazante SandersElizabeth Humphries avatar Elizabeth Humphriesorcid logoSimon Gladman avatar Simon Gladmanorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnna Syme avatar Anna Symeorcid logoMiaomiao Zhou avatar Miaomiao ZhouTorsten Seemann avatar Torsten SeemannAva Hoffman avatar Ava Hoffmanorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMateo Boudet avatar Mateo Boudetorcid logoBérénice Batut avatar Bérénice BatutNathan Dunn avatar Nathan DunnCandace Savonen avatar Candace SavonenRobert Meller avatar Robert Mellerorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoTeresa Müller avatar Teresa Müllerorcid logoLaura Leroi avatar Laura LeroiJasper Ouwerkerk avatar Jasper Ouwerkerk

Funding

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