<p>There seem to be WGS assemblies that can't be found in <a href="https://www.ncbi.nlm.nih.gov/assembly" rel="nofollow noreferrer">NCBI Assembly database</a>, e.g.: <a href="https://www.ncbi.nlm.nih.gov/nuccore/1779902990" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/nuccore/1779902990</a>. I guess that such assemblies also cannot be found in The assembly_summary.txt files that are described in <a href="https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt" rel="nofollow noreferrer">https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt</a>.</p>
<p>My current best guess is that each WGS assembly has a &quot;WGS master record&quot; in <a href="https://www.ncbi.nlm.nih.gov/nuccore" rel="nofollow noreferrer">NCBI Nuccore database</a>. To find all WGS assemblies of a taxon whose uid in <a href="https://www.ncbi.nlm.nih.gov/taxonomy" rel="nofollow noreferrer">NCBI Taxonomy database</a> is <code>1337</code>, search <a href="https://www.ncbi.nlm.nih.gov/nuccore" rel="nofollow noreferrer">NCBI Nuccore database</a> using <a href="https://biopython.org/docs/latest/api/Bio.Entrez.html" rel="nofollow noreferrer">Entrez</a> and the search term <code>&quot;wgs master&quot;[Properties] AND txid1337[orgn:exp]</code>.</p>

CC BY-SA 4.0
2020-11-08T18:59:34.680Z
2020-11-08T18:59:34.680Z
Oren Milman
<h3>Some background</h3>
<p>Similar to the OP of <a href="https://www.biostars.org/p/377840/" rel="nofollow noreferrer">https://www.biostars.org/p/377840/</a>, I would like to programmatically BLAST a sequence to a local database of all WGS assemblies.<br/>
Since this isn't feasible for the average biology lab server (correct me if I am wrong), I plan to use <a href="https://github.com/kblin/ncbi-acc-download" rel="nofollow noreferrer">ncbi-acc-download</a> to download all WGS assemblies of the species of interest (not a popular species like E. coli, so it should be feasible). Then, I will create a BLAST database for the downloaded assemblies and BLAST the sequence to it.</p>
<h3>My question</h3>
<p>How can I find all WGS assemblies accessions of a species?<br/></p>
<hr />
<br/>
<p>My current plan is to search the <a href="https://www.ncbi.nlm.nih.gov/assembly" rel="nofollow noreferrer">NCBI Assembly database</a> using <a href="https://biopython.org/docs/latest/api/Bio.Entrez.html" rel="nofollow noreferrer">Entrez</a> and a search term such as <code>&quot;wgs&quot;[Properties] AND txid1337[orgn:exp]</code>.<br/>
<strong>EDIT: IIUC, this approach might miss some WGS assemblies.</strong> See <a href="https://bioinformatics.stackexchange.com/a/14749/4868">my answer</a>.</p>
<p>I am worried (and thus ask for your help) this isn't the right approach because there seem to be at least 3 other places in which assemblies can be found:</p>
<ul>
<li>The assembly_summary.txt files that are described in <a href="https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt" rel="nofollow noreferrer">https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt</a>.</li>
<li><a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/Traces/wgs/</a>. <strong>This is the one I am most worried about.</strong> Both because it seems to have much more entries, and also because <a href="https://www.ncbi.nlm.nih.gov/genbank/wgs/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/genbank/wgs/</a> says: &quot;The public WGS projects are at the <a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/" rel="nofollow noreferrer">list of WGS projects</a> .&quot;</li>
<li><a href="ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/" rel="nofollow noreferrer">taxid2wgs.pl</a>. (As mentioned in <a href="https://www.biostars.org/p/377840/#471535" rel="nofollow noreferrer">https://www.biostars.org/p/377840/#471535</a>, this one seems to miss some assemblies.)</li>
</ul>

<assembly><phylogenetics><wgs>
How to find all WGS assemblies accessions of a species
# How to find all WGS assemblies accessions of a species

(Asked by: username_0 on 2020-11-05)

### Some background

Similar to the OP of <https://www.biostars.org/p/377840/>, I would like to programmatically BLAST a sequence to a local database of all WGS assemblies.  
Since this isn't feasible for the average biology lab server (correct me if I am wrong), I plan to use [ncbi-acc-download](https://github.com/kblin/ncbi-acc-download) to download all WGS assemblies of the species of interest (not a popular species like E. coli, so it should be feasible). Then, I will create a BLAST database for the downloaded assemblies and BLAST the sequence to it.

### My question

How can I find all WGS assemblies accessions of a species?

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My current plan is to search the [NCBI Assembly database](https://www.ncbi.nlm.nih.gov/assembly) using [Entrez](https://biopython.org/docs/latest/api/Bio.Entrez.html) and a search term such as `"wgs"[Properties] AND txid1337[orgn:exp]`.  
**EDIT: IIUC, this approach might miss some WGS assemblies.** See [my answer](https://bioinformatics.stackexchange.com/a/14749/4868).

I am worried (and thus ask for your help) this isn't the right approach because there seem to be at least 3 other places in which assemblies can be found:

* The assembly\_summary.txt files that are described in <https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt>.
* <https://www.ncbi.nlm.nih.gov/Traces/wgs/>. **This is the one I am most worried about.** Both because it seems to have much more entries, and also because <https://www.ncbi.nlm.nih.gov/genbank/wgs/> says: "The public WGS projects are at the [list of WGS projects](https://www.ncbi.nlm.nih.gov/Traces/wgs/) ."
* [taxid2wgs.pl](ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/). (As mentioned in <https://www.biostars.org/p/377840/#471535>, this one seems to miss some assemblies.)

**Tags:** assembly, phylogenetics, wgs

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## 1 answers

### Answer by username_0 on 2020-11-08. Score: 2

There seem to be WGS assemblies that can't be found in [NCBI Assembly database](https://www.ncbi.nlm.nih.gov/assembly), e.g.: <https://www.ncbi.nlm.nih.gov/nuccore/1779902990>. I guess that such assemblies also cannot be found in The assembly\_summary.txt files that are described in <https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt>.

My current best guess is that each WGS assembly has a "WGS master record" in [NCBI Nuccore database](https://www.ncbi.nlm.nih.gov/nuccore). To find all WGS assemblies of a taxon whose uid in [NCBI Taxonomy database](https://www.ncbi.nlm.nih.gov/taxonomy) is `1337`, search [NCBI Nuccore database](https://www.ncbi.nlm.nih.gov/nuccore) using [Entrez](https://biopython.org/docs/latest/api/Bio.Entrez.html) and the search term `"wgs master"[Properties] AND txid1337[orgn:exp]`.


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