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 logoCristóbal Gallardo avatar Cristóbal GallardoJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoHelena Rasche avatar Helena RascheDaniela Butano avatar Daniela Butanoorcid logoErwan Corre avatar Erwan CorreAva Hoffman avatar Ava HoffmanTorsten Seemann avatar Torsten Seemannorcid logoMiaomiao Zhou avatar Miaomiao ZhouNathan Dunn avatar Nathan Dunnorcid logoAnthony Bretaudeau avatar Anthony BretaudeauSimon Bray avatar Simon BrayRobert Meller avatar Robert Mellerorcid logoLaura Leroi avatar Laura Leroiorcid logoBérénice Batut avatar Bérénice BatutElizabeth Humphries avatar Elizabeth HumphriesDeepti Varshney avatar Deepti VarshneyFrederick Tan avatar Frederick Tanorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoPaul Zierep avatar Paul ZierepTeresa Müller avatar Teresa Müllerorcid logoStéphanie Robin avatar Stéphanie RobinCandace Savonen avatar Candace Savonenorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSimon Gladman avatar Simon GladmanKatherine Cox avatar Katherine CoxBazante Sanders avatar Bazante Sandersorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoBjörn Grüning avatar Björn GrüningNatalie Kucher avatar Natalie Kucherorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnna Syme avatar Anna SymeAnton Nekrutenko avatar Anton NekrutenkoYo Yehudi avatar Yo Yehudiorcid logoJonathan Kreplak avatar Jonathan Kreplak

Funding

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