Submitting SARS-CoV-2 sequences to ENA
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Requirements
Before diving into this slide deck, we recommend you to have a look at:
- Introduction to Galaxy Analyses
- Galaxy Basics for genomics: tutorial hands-on
The European Nucleotide Archive
ENA is:
- a FAIR and Open repository for sequence data (reads, assemblies, annotations)
- part of the International Nucleotide Sequence Database Collaboration (INSDC) with NCBI and DDJB
- the COVID-19 data portal repository for SARS-CoV-2 sequences
The European Nucleotide Archive and INSDC
SARS-CoV-2 sequences
Why is raw SARS-CoV-2 sequence data important?
- Allows reuse of data and reproducibility of analysis
- Enables discovery of minor allelic variants and intrahost variation
Minor allelic-variants can be used to detect intrahost variation. From Maier et al., 2021 doi.org/10.1101/2021.03.25.437046
What you need
Data:
- compressed fastq format (.fastq.gz, .fastq.bz2)
- human traces removed (tutorial)
Metadata:
- interactive metadata input (for a few submissions) or;
- metadata template spreadsheet (for bulk submissions)
Credentials:
- ENA Webin credentials in your Galaxy user information
Metadata
For the submission of SARS-CoV-2 reads ENA's metadata model requires:
- study, sample, experiment and run information
- additional information for viral samples (viral checklist)
Metadata
Metadata template spreadsheet:
- one sheet each for study, sample, experiment and run
- built-in controlled vocabulary
Thank You!
This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!
| Author(s) |
Miguel Roncoroni
|
| Reviewers |
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Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.