<p>The nomenclature is no longer being followed as NCBI is moving all the files to S3/Google cloud. <a href="https://github.com/saketkc/pysradb" rel="nofollow noreferrer">pysradb</a> allows you to fetch the metadata and get the URLs for each individual SRR. See examples in <a href="https://colab.research.google.com/drive/1tOVBg7vPnhTYNjyFQTvN0K9jGT3MyrVb" rel="nofollow noreferrer">this notebook</a>.</p>

<p>You can also download an entire project by doing:</p>

<pre><code>pysradb download -p &lt;SRP&gt;
</code></pre>

CC BY-SA 4.0
2020-01-22T22:58:48.517Z
2020-01-22T22:58:48.517Z
Saket Choudhary
<p>I would like to assign a URL/URI to accession runs (i.e. SRR IDs) from the NCBI short read archive.</p>

<p>In program listings, I used to list them as <code>ftp://</code> URLs, because they were available on their servers as such, e.g. <code>SRR3418242</code>:</p>

<pre><code>ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR341/SRR3418242/SRR3418242.sra
</code></pre>

<p>But this approach is deprecated, plus, not all runs are available this way anymore. The now recommended approach is to use <a href="https://www.ncbi.nlm.nih.gov/sra/docs/sradownload/" rel="nofollow noreferrer">sra-tools to download the data</a>. This tool takes the SRR Ids directly, i.e. <code>prefetch "SRR3418242"</code>, and resolves them to one of many possible locations (home directory, http, etc).</p>

<p>Is there an official URI scheme that can be used to reference accession runs from the short-read-archive ? I would like to disambiguate them from other types of files and URLs (S3 keys, http, file). For file manifests, spreadsheets, and publications, is there something similar to <code>srr://SRR3418242</code>?</p>

CC BY-SA 4.0
2019-03-21T22:21:20.623Z
No, there isn't something like srr:// and there won't be. ENA via aspera is almost always the preferred way to download data as long as ENA has it.
user172818
CC BY-SA 4.0
2019-03-22T19:40:40.013Z
Thanks. My concern is the namespace. I'd like to know a nomenclature which doesn't prescribe a particular software or particular read archive. As long as run numbers and sequence data agree on both archives...
init_js
<phylogenetics><sratoolkit>
What is the recognized way to reference accession data (.sra files) from NCBI as a URI?
# What is the recognized way to reference accession data (.sra files) from NCBI as a URI?

(Asked by: username_0 on 2019-03-21)

I would like to assign a URL/URI to accession runs (i.e. SRR IDs) from the NCBI short read archive.
In program listings, I used to list them as ftp:// URLs, because they were available on their servers as such, e.g. SRR3418242:
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR341/SRR3418242/SRR3418242.sra

But this approach is deprecated, plus, not all runs are available this way anymore. The now recommended approach is to use sra-tools to download the data. This tool takes the SRR Ids directly, i.e. prefetch "SRR3418242", and resolves them to one of many possible locations (home directory, http, etc).
Is there an official URI scheme that can be used to reference accession runs from the short-read-archive ? I would like to disambiguate them from other types of files and URLs (S3 keys, http, file). For file manifests, spreadsheets, and publications, is there something similar to srr://SRR3418242?

**Tags:** phylogenetics, sratoolkit
> **Comments:**
> **username_1**: No, there isn't something like srr:// and there won't be. ENA via aspera is almost always the preferred way to download data as long as ENA has it.  
> **username_0**: Thanks. My concern is the namespace. I'd like to know a nomenclature which doesn't prescribe a particular software or particular read archive. As long as run numbers and sequence data agree on both archives...  

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## 1 answers

### Answer by username_2 on 2020-01-22. Score: 1

The nomenclature is no longer being followed as NCBI is moving all the files to S3/Google cloud. pysradb allows you to fetch the metadata and get the URLs for each individual SRR. See examples in this notebook.
You can also download an entire project by doing:
pysradb download -p


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