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.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Material

JBrowse 1

Learn to use JBrowse v1 here.

Lesson Slides Hands-on Recordings Input dataset Workflows
Hands-on: Hands-on: Bacterial Genome Annotation
Hands-on: Hands-on: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
Hands-on: Hands-on: Genome annotation with Prokka
Hands-on: Hands-on: Genomic Data Visualisation with JBrowse
Hands-on: Hands-on: Identification of AMR genes in an assembled bacterial genome
Hands-on: Hands-on: Making sense of a newly assembled genome
Hands-on: Hands-on: Microbial Variant Calling
Hands-on: Hands-on: Refining Genome Annotations with Apollo (prokaryotes)
Hands-on: Hands-on: SARS-CoV-2 Viral Sample Alignment and Variant Visualization
Hands-on: Hands-on: Genome annotation with Funannotate
Hands-on: Hands-on: Genome annotation with Maker (short)
Hands-on: Hands-on: Genome annotation with Maker
Hands-on: Hands-on: Refining Genome Annotations with Apollo (eukaryotes)

MAKER

Genome Annotation with MAKER.

Lesson Slides Hands-on Recordings Input dataset Workflows
Hands-on: Hands-on: Genome annotation with Maker (short)
Hands-on: Hands-on: 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
Hands-on: Hands-on: InterMine integration with Galaxy

Apollo v2

Apollo is a collaborative, real time genome annotation editor.

Lesson Slides Hands-on Recordings Input dataset Workflows
Hands-on: Hands-on: Refining Genome Annotations with Apollo (prokaryotes)
Hands-on: Hands-on: Refining Genome Annotations with Apollo (eukaryotes)

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Avans Hogeschool avatar Avans HogeschoolNatalie Kucher avatar Natalie Kucherorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton NekrutenkoBazante Sanders avatar Bazante Sandersorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnthony Bretaudeau avatar Anthony BretaudeauDaniela Butano avatar Daniela Butanoorcid logoErwan Corre avatar Erwan Correorcid logoAlexandre Cormier avatar Alexandre CormierNathan Dunn avatar Nathan DunnRobert Meller avatar Robert Mellerorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSimon Gladman avatar Simon Gladmanorcid logoBérénice Batut avatar Bérénice BatutYo Yehudi avatar Yo Yehudiorcid logoAnna Syme avatar Anna Symeorcid logoSaskia Hiltemann avatar Saskia HiltemannCandace Savonen avatar Candace SavonenKatherine Cox avatar Katherine Coxorcid logoLaura Leroi avatar Laura Leroiorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoStéphanie Robin avatar Stéphanie RobinAva Hoffman avatar Ava HoffmanElizabeth Humphries avatar Elizabeth HumphriesTorsten Seemann avatar Torsten SeemannFrederick Tan avatar Frederick Tan

Funders

This material was funded by:

National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space avatar NHGRI ANVILABRomics avatar ABRomicsEuroScienceGateway avatar EuroScienceGatewayNational Human Genome Research Institute Genomic Data Science Community Network avatar NHGRI GDS Community NetworkGallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries