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 logoAnna Syme avatar Anna SymeBazante Sanders avatar Bazante Sandersorcid logoBérénice Batut avatar Bérénice Batutorcid logoMateo Boudet avatar Mateo Boudetorcid logoJonathan Kreplak avatar Jonathan KreplakRobert Meller avatar Robert MellerTorsten Seemann avatar Torsten SeemannYo Yehudi avatar Yo Yehudiorcid logoLaura Leroi avatar Laura Leroiorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSimon Gladman avatar Simon GladmanFrederick Tan avatar Frederick Tanorcid logoDelphine Lariviere avatar Delphine LariviereDaniela Butano avatar Daniela Butanoorcid logoAlexandre Cormier avatar Alexandre CormierElizabeth Humphries avatar Elizabeth Humphriesorcid logoCristóbal Gallardo avatar Cristóbal GallardoDeepti Varshney avatar Deepti Varshneyorcid logoErwan Corre avatar Erwan CorreJasper Ouwerkerk avatar Jasper OuwerkerkNathan Dunn avatar Nathan Dunnorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoHelena Rasche avatar Helena Rascheorcid logoBjörn Grüning avatar Björn GrüningKatherine Cox avatar Katherine CoxTeresa Müller avatar Teresa MüllerSimon Bray avatar Simon BrayAnton Nekrutenko avatar Anton NekrutenkoAva Hoffman avatar Ava HoffmanNatalie Kucher avatar Natalie Kucherorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoPaul Zierep avatar Paul Ziereporcid logoSaskia Hiltemann avatar Saskia HiltemannCandace Savonen avatar Candace Savonen

Funding

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