Workshops and courses

Learning Pathway Genome annotation for eukaryotes

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Date: No date given

Learn how to annotate an eukaryotic genome sequence: identify repeated regions, find the position and function of genes, and even set up a manual curation environment with Apollo.

Keywords: eukaryote, genome-annotation

Learning objectives:

  • Annotate genome with Funannotate
  • Annotate lncRNAs with FEELnc
  • Classify lncRNAs according to their location
  • Evaluate annotation quality with BUSCO
  • Export refined genome annotations
  • Learn how to load JBrowse data into Apollo
  • Learn how to manually refine genome annotations within Apollo
  • Load a genome into Galaxy
  • Load data (genome assembly, annotation and mapped RNASeq) into Galaxy
  • Load genome into Galaxy
  • Perform a transcriptome assembly with StringTie
  • Perform functional annotation using EggNOG-mapper and InterProScan
  • Update genome annotation with lncRNAs
  • Use Red and RepeatMasker to soft-mask a newly assembled genome
  • View annotations in JBrowse

Event types:

  • Workshops and courses

Sponsors: ELIXIR Europe

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