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:

Simon Bray avatar Simon Brayorcid logoSaskia Hiltemann avatar Saskia HiltemannTorsten Seemann avatar Torsten SeemannJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoTeresa Müller avatar Teresa Müllerorcid logoAlexandre Cormier avatar Alexandre CormierDaniela Butano avatar Daniela Butanoorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBjörn Grüning avatar Björn GrüningElizabeth Humphries avatar Elizabeth Humphriesorcid logoErwan Corre avatar Erwan Correorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoPaul Zierep avatar Paul Ziereporcid logoAnthony Bretaudeau avatar Anthony BretaudeauKatherine Cox avatar Katherine Coxorcid logoHelena Rasche avatar Helena RascheCandace Savonen avatar Candace SavonenBazante Sanders avatar Bazante SandersRobert Meller avatar Robert Mellerorcid logoSimon Gladman avatar Simon GladmanFrederick Tan avatar Frederick TanYo Yehudi avatar Yo YehudiNatalie Kucher avatar Natalie Kucherorcid logoBérénice Batut avatar Bérénice Batutorcid logoDeepti Varshney avatar Deepti VarshneyAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMateo Boudet avatar Mateo Boudetorcid logoLaura Leroi avatar Laura Leroiorcid logoAnna Syme avatar Anna Symeorcid logoStéphanie Robin avatar Stéphanie RobinAva Hoffman avatar Ava HoffmanNathan Dunn avatar Nathan Dunn

Funding

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