Keywords: beginner

Learning objectives:

• Annotate genome with Funannotate
• Annotate genome with Prokka
• Annotate lncRNAs with FEELnc
• Classify lncRNAs according to their location
• Compare repositories to find which are suitable for your data
• Connect different parts of the Research Object using identifiers
• Construct an RO-Crate by hand using JSON
• Create a custom, annotated RO-Crate
• Describe each part of the Research Object
• Evaluate annotation quality with BUSCO
• Export refined genome annotations
• Find out what the requirements are for submitting
• Generate a workflow test using Planemo
• Learn about metadata and findability
• Learn basic JSON-LD to create FAIR metadata
• Learn best practices in data management
• Learn how to introduce computational reproducibility in your research
• Learn how to load JBrowse data into Apollo
• Learn how to manually refine genome annotations within Apollo
• Learn how to support system and content curation
• Learn the FAIR principles
• Load a genome into Galaxy
• Load data (genome assembly, annotation and mapped RNASeq) into Galaxy
• Load genome into Galaxy
• Locate bioimage data repositories
• Perform a transcriptome assembly with StringTie
• Perform functional annotation using EggNOG-mapper and InterProScan
• Recognise the relationship between FAIR and Open data
• Understand how testing can be automated with GitHub Actions
• Understanding, viewing and creating Galaxy Workflow Run Crates
• Update genome annotation with lncRNAs
• Use ORCIDs and other linked data to annotate datasets contained within the crate
• Use Red and RepeatMasker to soft-mask a newly assembled genome
• Validate your genes and create an official gene set from them.
• View annotations in JBrowse

Event types:

• Workshops and courses

Sponsors: ELIXIR Europe

Scientific topics: Genomics, Microbiology, Gene and protein families, Sequence analysis