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 logoSaskia Hiltemann avatar Saskia HiltemannDaniela Butano avatar Daniela Butanoorcid logoHelena Rasche avatar Helena RascheElizabeth Humphries avatar Elizabeth Humphriesorcid logoErwan Corre avatar Erwan CorreNathan Dunn avatar Nathan Dunnorcid logoDelphine Lariviere avatar Delphine LariviereJasper Ouwerkerk avatar Jasper OuwerkerkAnton Nekrutenko avatar Anton NekrutenkoAva Hoffman avatar Ava Hoffmanorcid logoTeresa Müller avatar Teresa Müllerorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAnthony Bretaudeau avatar Anthony BretaudeauTorsten Seemann avatar Torsten Seemannorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoBérénice Batut avatar Bérénice Batutorcid logoBjörn Grüning avatar Björn GrüningSimon Bray avatar Simon BrayKatherine Cox avatar Katherine CoxNatalie Kucher avatar Natalie Kucherorcid logoMateo Boudet avatar Mateo Boudetorcid logoPaul Zierep avatar Paul Ziereporcid logoAnna Syme avatar Anna SymeRobert Meller avatar Robert Mellerorcid logoCristóbal Gallardo avatar Cristóbal GallardoBazante Sanders avatar Bazante Sandersorcid logoSimon Gladman avatar Simon GladmanCandace Savonen avatar Candace Savonenorcid logoLaura Leroi avatar Laura Leroiorcid logoJonathan Kreplak avatar Jonathan KreplakFrederick Tan avatar Frederick Tanorcid logoAlexandre Cormier avatar Alexandre CormierYo Yehudi avatar Yo Yehudi

Funding

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