name: inverse layout: true class: center, middle, inverse <div class="my-header"><span> <a href="/training-material/topics/galaxy-interface" title="Return to topic page" ><i class="fa fa-level-up" aria-hidden="true"></i></a> <a class="nav-link" href="https://github.com/galaxyproject/training-material/edit/main/topics/galaxy-interface/tutorials/upload-data-to-ena/slides.html"><i class="fa fa-pencil" aria-hidden="true"></i></a> </span></div> <div class="my-footer"><span> <img src="/training-material/assets/images/GTN-60px.png" alt="Galaxy Training Network" style="height: 40px;"/> </span></div> --- <img src="/training-material/assets/images/GTN.png" alt="Galaxy Training Network" class="cover-logo"/> # Submitting SARS-CoV-2 sequences to ENA <div markdown="0"> <div class="contributors-line"> Authors: <a href="/training-material/hall-of-fame/roncoronimiguel/" class="contributor-badge contributor-roncoronimiguel"><img src="https://avatars.githubusercontent.com/roncoronimiguel?s=27" alt="Avatar">Miguel Roncoroni</a> </div> </div> <!-- modified date --> <div class="footnote" style="bottom: 8em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: Aug 10, 2021</div> <!-- other slide formats (video and plain-text) --> <div class="footnote" style="bottom: 6em;"> <i class="fas fa-file-alt" aria-hidden="true"></i><span class="visually-hidden">text-document</span><a href="slides-plain.html"> Plain-text slides</a> </div> <!-- usage tips --> <div class="footnote" style="bottom: 2em;"> <strong>Tip: </strong>press <kbd>P</kbd> to view the presenter notes | <i class="fa fa-arrows" aria-hidden="true"></i><span class="visually-hidden">arrow-keys</span> Use arrow keys to move between slides </div> ??? 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Useful when presenting. --- ### <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 --- ### 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[  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](https://virological.org/t/global-framework-for-sars-cov-2-data-analysis-application-to-intrahost-variation-part-1/623) ] .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](https://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](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[  ] --- ### 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 .left[ Interactive metadata input in Galaxy: ]  --- ### 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 .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 ]  --- --- ### <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) --- ## 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! <div markdown="0"> <div class="contributors-line"> Authors: <a href="/training-material/hall-of-fame/roncoronimiguel/" class="contributor-badge contributor-roncoronimiguel"><img src="https://avatars.githubusercontent.com/roncoronimiguel?s=27" alt="Avatar">Miguel Roncoroni</a> </div> </div> <div style="display: flex;flex-direction: row;align-items: center;justify-content: center;"> <img src="/training-material/assets/images/GTN.png" alt="Galaxy Training Network" style="height: 100px;"/> </div> <a rel="license" href="https://creativecommons.org/licenses/by/4.0/"> This material is licensed under the Creative Commons Attribution 4.0 International License</a>.