Submitting SARS-CoV-2 sequences to ENA

Contributors

Authors: Miguel Roncoroni

Objectives

• Introduce the European Nucleotide Archive (ENA)

• Learn the requirements to submit raw SARS-CoV-2 sequences to ENA in Galaxy

• Overview ENA’s metadata model and how metadata objects are linked

The European Nucleotide Archive

.pull-left[

.left[ 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 ] ] .pull-right[

The European Nucleotide Archive and INSDC ]

SARS-CoV-2 sequences

.left[ 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 ] .image-40[ ]

.reduce70[Minor allelic-variants can be used to detect intrahost variation. From Maier et al., 2021 doi.org/10.1101/2021.03.25.437046]

Submitting reads with Galaxy

.left[ Why use Galaxy to submit to ENA?

• intuitive graphical user interface (GUI)
• simple metadata input via a template spreadsheet or interactively
• no bioinformatics skills needed ] .image-75[ ]

Submission overview

.image-100[ ] —

What you need

.left[ 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 ] .left[ ] —

Metadata

.left[ 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

.left[ Interactive metadata input in Galaxy: ] —

Metadata

.left[ Metadata template spreadsheet:

• one sheet each for study, sample, experiment and run
• built-in controlled vocabulary ] —

Metadata

.left[

• Different metadata objects are linked using Aliases
• Aliases must be unique ] —

Aliases

.left[ Aliases link metadata objects:

• Experiments are linked to Study and Samples
• Runs are linked to Experiments ] —

Aliases

.left[ Aliases link metadata objects:

• Experiments are linked to Study and Samples
• Runs are linked to Experiments ] —

Aliases

.left[ Aliases link metadata to data:

• Data (filename.fastq.gz) is linked to Run Alias ] —

Key Points

• ENA is a FAIR data repository for SARS-CoV-2 raw and assembled nucleotide data
• You can easily submit reads to ENA using Galaxy's ENA upload tool (GUI, no bioinformatic skills needed)

Thank you!