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Merge pull request #5 from blankenberg/sra2
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add zenodo for fasta
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mvdbeek committed Jun 24, 2020
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19 changes: 18 additions & 1 deletion topics/variant-analysis/tutorials/sars-cov-2/tutorial.md
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layout: tutorial_hands_on

title: "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis"
zenodo_link: ''
zenodo_link: 'http://zenodo.org/record/3906454'
questions:
- Learn how to get and use data from the Sequence Read Archive in Galaxy.
objectives:
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However, if you retrieved the datasets used in this tutorial's examples above, then you are ready to run the SARS-CoV-2 variant analysis below.

# Get the reference genome data

The reference genome data for today is for SARS-CoV-2, "Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome", having the accession ID of NC_045512.2.

This data is available from Zenodo using the following [link](https://doi.org/10.5281/zenodo.3906454).

> ### {% icon hands_on %} Hands-on: Get the reference genome data
>
> 1. Import the following file into your history:
>
> ```
> https://zenodo.org/record/3906454/files/NC_045512.2.fasta
> ```
>
> {% include snippets/import_via_link.md %}
>
{: .hands_on}

# Variant Analysis of SARS-Cov-2 sequencing data

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