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.

For any question or discussions related to this topic, or to connect with others in the community, please visit the community chat:

comment   Community Matrix Chat

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 Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
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:

Frederick Tan avatar Frederick TanTorsten Seemann avatar Torsten SeemannRobert Meller avatar Robert Mellerorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoMateo Boudet avatar Mateo BoudetElizabeth Humphries avatar Elizabeth Humphriesorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAnna Syme avatar Anna Symeorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSaskia Hiltemann avatar Saskia HiltemannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHelena Rasche avatar Helena RascheBazante Sanders avatar Bazante SandersAva Hoffman avatar Ava Hoffmanorcid logoSimon Gladman avatar Simon Gladmanorcid logoBérénice Batut avatar Bérénice BatutDaniela Butano avatar Daniela Butanoorcid logoDelphine Lariviere avatar Delphine LariviereCandace Savonen avatar Candace SavonenNathan Dunn avatar Nathan Dunnorcid logoAlexandre Cormier avatar Alexandre CormierYo Yehudi avatar Yo YehudiNatalie Kucher avatar Natalie Kucherorcid logoLaura Leroi avatar Laura Leroiorcid logoErwan Corre avatar Erwan CorreKatherine Cox avatar Katherine Cox

Funding

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