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 logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMiaomiao Zhou avatar Miaomiao ZhouNathan Dunn avatar Nathan Dunnorcid logoJonathan Kreplak avatar Jonathan KreplakTorsten Seemann avatar Torsten SeemannCandace Savonen avatar Candace SavonenElizabeth Humphries avatar Elizabeth HumphriesSimon Bray avatar Simon Brayorcid logoMateo Boudet avatar Mateo BoudetJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoHelena Rasche avatar Helena RascheRobert Meller avatar Robert MellerFrederick Tan avatar Frederick Tanorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoTeresa Müller avatar Teresa Müllerorcid logoSimon Gladman avatar Simon GladmanKatherine Cox avatar Katherine CoxAnton Nekrutenko avatar Anton NekrutenkoDaniela Butano avatar Daniela Butanoorcid logoPaul Zierep avatar Paul Ziereporcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoLaura Leroi avatar Laura Leroiorcid logoBérénice Batut avatar Bérénice BatutNatalie Kucher avatar Natalie Kucherorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBjörn Grüning avatar Björn Grüningorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAnna Syme avatar Anna SymeBazante Sanders avatar Bazante Sandersorcid logoErwan Corre avatar Erwan CorreAva Hoffman avatar Ava HoffmanYo Yehudi avatar Yo Yehudi

Funding

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