ENA Sequence Retrieval Course

13 March 2018
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus , Hinxton , United Kingdom
Involved Work Packages
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This free course will introduce users to the powerful search and retrieval methods available within ENA (European Nucleotide Archive) for annotated sequences, genomes, raw data and metadata, as well as download options from the ENA browser and an introduction to the various ENA browser tools. There will also be a section on cross references and how to retrieve accessions for other resources linked to the primary data in ENA. There will be time at the end of the course for users to present their own use cases or request specific help for their own queries, enabling them to perform searches to enhance their own research.

Workshop content:

Advanced search and ENA portal API

  • Differences between the two
  • Data portals and the API
  • Building search queries
  • Reports
  • Metadata and sequence retrieval

Downloading sequence data from the ENA browser

  • Single and range accessions
  • Download via taxon and/or project page

Downloading run/analysis data

  • Single accession from the browser (read and analysis tables)
  • FTP vs Aspera
  • ENA FTP downloader
    • By accession
    • By report

ENA Browser Tools

  • Installation and setup
  • Looking at the two tools and the options
  • Downloading an assembly using enaDataGet
  • Downloading an experiment using enaDataGet
  • Downloading data for a study using enaGroupGet
  • Downloading all sequences for a taxon using enaGroupGet

Exploring links between data

  • Links between ENA data types
  • Links from between ENA and other resources

Specific use cases – discussion and assistance

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