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:

Ava Hoffman avatar Ava Hoffmanorcid logoMiaomiao Zhou avatar Miaomiao ZhouRobert Meller avatar Robert Mellerorcid logoBjörn Grüning avatar Björn GrüningKatherine Cox avatar Katherine CoxBazante Sanders avatar Bazante Sandersorcid logoMateo Boudet avatar Mateo BoudetSimon Bray avatar Simon BrayNatalie Kucher avatar Natalie Kucherorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnthony Bretaudeau avatar Anthony BretaudeauNathan Dunn avatar Nathan Dunnorcid logoAnna Syme avatar Anna Symeorcid logoSimon Gladman avatar Simon GladmanDaniela Butano avatar Daniela Butanoorcid logoPaul Zierep avatar Paul Ziereporcid logoTeresa Müller avatar Teresa MüllerCandace Savonen avatar Candace Savonenorcid logoHelena Rasche avatar Helena RascheYo Yehudi avatar Yo YehudiJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoErwan Corre avatar Erwan Correorcid logoStéphanie Robin avatar Stéphanie RobinTorsten Seemann avatar Torsten Seemannorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBérénice Batut avatar Bérénice Batutorcid logoDelphine Lariviere avatar Delphine LariviereFrederick Tan avatar Frederick Tanorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoSaskia Hiltemann avatar Saskia HiltemannElizabeth Humphries avatar Elizabeth Humphriesorcid logoLaura Leroi avatar Laura Leroi

Funding

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