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:

orcid logoSimon Gladman avatar Simon GladmanDaniela Butano avatar Daniela ButanoAvans Hogeschool avatar Avans HogeschoolCandace Savonen avatar Candace SavonenRobert Meller avatar Robert Mellerorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoLaura Leroi avatar Laura LeroiFrederick Tan avatar Frederick Tanorcid logoBérénice Batut avatar Bérénice BatutTorsten Seemann avatar Torsten Seemannorcid logoMateo Boudet avatar Mateo BoudetElizabeth Humphries avatar Elizabeth Humphriesorcid logoErwan Corre avatar Erwan Correorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnna Syme avatar Anna SymeYo Yehudi avatar Yo YehudiNathan Dunn avatar Nathan DunnKatherine Cox avatar Katherine Coxorcid logoSaskia Hiltemann avatar Saskia HiltemannAva Hoffman avatar Ava Hoffmanorcid logoDelphine Lariviere avatar Delphine LariviereNatalie Kucher avatar Natalie KucherAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBazante Sanders avatar Bazante Sandersorcid logoHelena Rasche avatar Helena Rascheorcid logoStéphanie Robin avatar Stéphanie Robin

Funders

This material was funded by:

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