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 logoMateo Boudet avatar Mateo BoudetNathan Dunn avatar Nathan Dunnorcid logoJonathan Kreplak avatar Jonathan KreplakElizabeth Humphries avatar Elizabeth HumphriesKatherine Cox avatar Katherine Coxorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoErwan Corre avatar Erwan CorreDaniela Butano avatar Daniela ButanoFrederick Tan avatar Frederick Tanorcid logoSaskia Hiltemann avatar Saskia HiltemannTorsten Seemann avatar Torsten SeemannSimon Bray avatar Simon Brayorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMiaomiao Zhou avatar Miaomiao ZhouNatalie Kucher avatar Natalie Kucherorcid logoBérénice Batut avatar Bérénice BatutAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHelena Rasche avatar Helena Rascheorcid logoAnna Syme avatar Anna Symeorcid logoDeepti Varshney avatar Deepti VarshneyBazante Sanders avatar Bazante Sandersorcid logoSimon Gladman avatar Simon GladmanCandace Savonen avatar Candace Savonenorcid logoStéphanie Robin avatar Stéphanie RobinRobert Meller avatar Robert MellerJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoLaura Leroi avatar Laura Leroiorcid logoPaul Zierep avatar Paul Ziereporcid logoTeresa Müller avatar Teresa MüllerYo Yehudi avatar Yo Yehudiorcid logoAlexandre Cormier avatar Alexandre CormierAva Hoffman avatar Ava Hoffmanorcid logoBjörn Grüning avatar Björn Grüning

Funding

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