Submitting SARS-CoV-2 sequences to ENA

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# Submitting SARS-CoV-2 sequences to ENA

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			<li>
				<a href="/training-material/hall-of-fame/roncoronimiguel/" class="contributor-badge contributor-roncoronimiguel"><img src="https://avatars.githubusercontent.com/roncoronimiguel?s=36" alt="Miguel Roncoroni avatar" width="36" class="avatar" />
    Miguel Roncoroni</a></li>
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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)
    - Galaxy Basics for genomics: [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/introduction/tutorials/galaxy-intro-101/tutorial.html)

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### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> 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

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### 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](https://www.covid19dataportal.org/) repository for SARS-CoV-2 sequences
]
]
.pull-right[
![ENA-FAIR](../../images/upload-data-to-ena/ENA-FAIR.png)

The European Nucleotide Archive and INSDC
]

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## 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](https://virological.org/t/global-framework-for-sars-cov-2-data-analysis-application-to-intrahost-variation-part-1/623)
]
.image-40[
![Intrahost variation](../../images/upload-data-to-ena/intra-host.png)
]

.reduce70[Minor allelic-variants can be used to detect intrahost variation. From Maier et al., 2021 [doi.org/10.1101/2021.03.25.437046](https://doi.org/10.1101/2021.03.25.437046)]
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### 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[![upload-tool](../../images/upload-data-to-ena/upload-tool.png)
]

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### Submission overview
.image-100[
![reads-submission](../../images/upload-data-to-ena/reads_submission.png)
]
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### What you need
.left[
Data:
- compressed fastq format (*.fastq.gz, *.fastq.bz2)
- human traces removed ([tutorial](https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html))

Metadata:
- interactive metadata input (for a few submissions) or;
- metadata [template spreadsheet](https://drive.google.com/file/d/1Gx78GKh58PmRjdmJ05DBbpObAL-3oUFX/view?usp=sharing) (for bulk submissions)

Credentials:
- [ENA Webin credentials](https://www.ebi.ac.uk/ena/submit/sra/#registration) in your Galaxy user information
]
.left[
![ENA-credentials](../../images/upload-data-to-ena/ENA-credentials.png)
]
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### Metadata
.left[
For the submission of SARS-CoV-2 reads [ENA's metadata model](https://ena-docs.readthedocs.io/en/latest/submit/general-guide/metadata.html) requires:
- study, sample, experiment and run information
- additional information for viral samples ([viral checklist](https://www.ebi.ac.uk/ena/browser/view/ERC000033))
]
![metadata-model](../../images/upload-data-to-ena/metadata_model_reads.png)

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### Metadata
.left[
Interactive metadata input in Galaxy:
]
![interactive metadata](../../images/upload-data-to-ena/interactive_metadata.png)
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### Metadata
.left[
Metadata [template spreadsheet](https://drive.google.com/file/d/1Gx78GKh58PmRjdmJ05DBbpObAL-3oUFX/view?usp=sharing):
- one sheet each for study, sample, experiment and run
- built-in controlled vocabulary
]
![metadata_template](../../images/upload-data-to-ena/metadata_template.png)
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### Metadata
.left[
- Different metadata objects are linked using Aliases
- Aliases must be unique
]
![metadata-model](../../images/upload-data-to-ena/metadata_model_reads.png)
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### Aliases
.left[
Aliases link metadata objects:
- Experiments are linked to Study and Samples
- Runs are linked to Experiments
]
![study-sample](../../images/upload-data-to-ena/study_sample_exp.png)
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### Aliases
.left[
Aliases link metadata objects:
- Experiments are linked to Study and Samples
- Runs are linked to Experiments
]
![exp-run](../../images/upload-data-to-ena/exp_run.png)
---

### Aliases
.left[
Aliases link metadata to data:
- Data (filename.fastq.gz) is linked to Run Alias
]
![data-metadata](../../images/upload-data-to-ena/data_metadata.png)
---

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### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> 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)

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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	<tr>
		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
		<td>
			<a href="/training-material/hall-of-fame/roncoronimiguel/" class="contributor-badge contributor-roncoronimiguel"><img src="https://avatars.githubusercontent.com/roncoronimiguel?s=36" alt="Miguel Roncoroni avatar" width="36" class="avatar" />
    Miguel Roncoroni</a>
		</td>
	</tr>

<tr class="reviewers">
		<td><abbr title="These people reviewed this material for accuracy and correctness">Reviewers</abbr></td>
		<td>
			<a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-badge-small contributor-bgruening"><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/beatrizserrano/" class="contributor-badge contributor-badge-small contributor-beatrizserrano"><img src="https://avatars.githubusercontent.com/beatrizserrano?s=36" alt="Beatriz Serrano-Solano avatar" width="36" class="avatar" /></a></td>
	</tr>

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Tutorial Content is licensed under <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.<br/>