Answers.Body: <p>Remember not to omit the 'clarification' that in addition to Pango lineages, GISAID clades, Nextstrain clades there is also the WHO nomenclature. We could designate the <code>Bioinformatics StackExchange monophyly</code>, surely there is room for one more nomenclature?</p>
  <p>Here's the WHO's response copied and uploaded from <a href="https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/" rel="nofollow noreferrer">here</a></p>
  <p><a href="https://i.sstatic.net/ovWqZ.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ovWqZ.jpg" alt="enter image description here" /></a></p>
  <p>Just  to mention NCBI has adopted the Pango lineage nomenclature available on all of its sequences available via <a href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&amp;VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202%20(SARS-CoV-2),%20taxid:2697049&amp;CollectionDate_dr=1950-01-01T00:00:00Z%20TO%20NOW&amp;CreateDate_dt=1950-01-01T00:00:00Z%20TO%20NOW" rel="nofollow noreferrer">this link</a></p>
  <p>I thought that Omicron was Pango lineage B12, or perhaps B.1.2? Oh I see it has been reclassified following further sequence data.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-25T18:55:53.113Z
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Answers.LastEditDate: 2022-02-25T19:29:07.387Z
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Answers.Body: <p>This information is now easily available in JSON format here: <a href="https://github.com/corneliusroemer/pango-sequences/blob/main/data/pango-consensus-sequences_summary.json" rel="nofollow noreferrer">https://github.com/corneliusroemer/pango-sequences/blob/main/data/pango-consensus-sequences_summary.json</a>. It's one big dictionary of dictionaries with Pango lineage names as outer keys and corresponding Nextstrain clades accessible via inner key:</p>
  <pre class="lang-json prettyprint-override"><code>{
   &quot;A&quot;: {
    &quot;lineage&quot;: &quot;A&quot;,
    &quot;nextstrainClade&quot;: &quot;19B&quot;,
    &quot;nucSubstitutions&quot;: [
     &quot;C8782T&quot;,
     &quot;T28144C&quot;
    ],
    ...
   },
   &quot;A.1&quot;: {
    &quot;lineage&quot;: &quot;A.1&quot;,
    &quot;unaliased&quot;: &quot;A.1&quot;,
    &quot;nextstrainClade&quot;: &quot;19B&quot;,
    ...
   },
   ...
  }
  </code></pre>
  <p>It's straightforward to convert this to a TSV mapping using just minimal scripting.</p>
  <p>Beware that not all Pango lineages pre-Omicron are contained therein. Small ones are missing currently.</p>
  <p>Disclaimer: I created the repo.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-02-13T15:21:52.763Z
Answers.LastActivityDate: 2023-02-13T15:21:52.763Z
Answers.UserDisplayName: Cornelius Roemer
Answers.Body: <p>A comment from a Nextclade's user satisfies my actual needs, I will post it here for future reference:</p>
  <blockquote>
  <p>Hi - one possible source is the metadata file for UCSC’s daily-updated tree of public SARS-CoV-2 sequences:</p>
  </blockquote>
  <pre><code>https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/public-latest.metadata.tsv.gz
  </code></pre>
  <blockquote>
  <p>It’s a big file – almost 3 million lines – because there are about 3M sequences in GenBank &amp; COG-UK at this point and that number will probably grow. The last two columns of the file (10th &amp; 11th) are the Nextstrain clade and Pango lineage assigned to each sequence based on its placement in the UCSC/UShER tree and the tree’s annotation of where each clade/lineage starts.</p>
  </blockquote>
  <blockquote>
  <p>This command will make a file relating each Nextstrain clade to at least one lineage (often to a lot of lineages, especially for Delta):</p>
  </blockquote>
  <pre><code>gunzip -c public-latest.metadata.tsv.gz | cut -f 10,11 | sort -u &gt; cladeToLineages.tsv
  </code></pre>
  <blockquote>
  <p>Some Pango lineages have no public sequences (only GISAID sequences, which can’t be shared at a public URL), so those lineages will be missing from that file. Some older lineages are not monophyletic on the UCSC/UShER tree, so those lineages are not annotated and will be missing. (In total, ~200 / ~1500 are missing.)</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-12-08T16:25:26.693Z
Answers.LastActivityDate: 2021-12-08T16:25:26.693Z
Answers.UserDisplayName: aechchiki
Body: <p>Is there any annotation file providing correspondence between <a href="https://clades.nextstrain.org/" rel="nofollow noreferrer">Nextclade</a> and <a href="https://cov-lineages.org/resources/pangolin.html" rel="nofollow noreferrer">Pangolin</a> variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from <a href="https://www.epicov.org" rel="nofollow noreferrer">Gisaid</a> with both these?</p>
  <p>For the moment I could only find:</p>
  <ul>
  <li><a href="https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv" rel="nofollow noreferrer">Nextclade's clade definitions</a></li>
  <li><a href="https://raw.githubusercontent.com/cov-lineages/pango-designation/master/lineages.csv" rel="nofollow noreferrer">Pangolin's lineage designations</a></li>
  </ul>
  <p>What I'm looking for is an annotation as follows:</p>
  <pre><code>lineage    clade
  AY.43      21J 
  AY.4       21J
  ...        ...
  </code></pre>
  <p>The idea is to generate a table as follows:</p>
  <pre><code>genome                                 lineage    clade
  hCoV-19/Germany/BW-RKI-I-195742/2021   AY.43      21J
  ...                                    ...        ...
  </code></pre>
  <p>The way I proceed now is the following:</p>
  <ul>
  <li>Parse the Pangolin's lineage designation file to find a target genome</li>
  <li>Look for the target genome in Gisaid (for quality check)</li>
  <li>Parse the metadata associated to the selected genome to get the lineage for verification (only Pangolin lineage is reported)</li>
  </ul>
  <p>These steps allow me to build the first part of the table:</p>
  <pre><code>genome                                 lineage    
  hCoV-19/Germany/BW-RKI-I-195742/2021   AY.43      
  ...                                    ...  
  </code></pre>
  <p>Then:</p>
  <ul>
  <li>Paste the genome to Nextclade, wait for the analysis to be completed</li>
  <li>Report the calculated clade</li>
  </ul>
  <p>With this information, I can then build the table:</p>
  <pre><code>genome                                 lineage    clade
  hCoV-19/Germany/BW-RKI-I-195742/2021   AY.43      21J
  ...                                    ...        ...
  </code></pre>
  <p>The idea behind this is that both lineages and clades can be used for &quot;tagging&quot; a genome, depending on the aim (a given clade e.g. 21J includes many lineages e.g. AY.43 and AY.4 in the example above) and that I don't enjoy manual and error-prone procedures;) Thanks for your input.</p>
  <hr />
  <p>The GISAID nomenclature via Nextstrain and overall tree is presented <a href="https://www.gisaid.org/phylodynamics/global/nextstrain/" rel="nofollow noreferrer">here</a></p>
  <p>(Crossposted on <a href="https://discussion.nextstrain.org/t/correspondance-of-sars-cov-2-annotations-nextclade-pangolin/883" rel="nofollow noreferrer">Nextstrain's discord forum</a>)</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-13T17:37:25.897Z
Comments.Text: The problem is that there's no one to one mapping between pango lineages and Nextstrain clades. One could generate the mapping from the Nextclade reference tree, there most tips have a pango lineage and a Nextstrain clades, and almost all pangos lineages appear in that tree. Other option is to use the open data metadata TSV from Nextstrain, same info.
Comments.UserDisplayName: Cornelius Roemer
Tags: <phylogenetics><sequence-annotation><covid-19><variants>
Title: Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)
ThreadText: # Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)
  
  (Asked by: username_0 on 2021-12-03)
  
  Is there any annotation file providing correspondence between [Nextclade](https://clades.nextstrain.org/) and [Pangolin](https://cov-lineages.org/resources/pangolin.html) variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from [Gisaid](https://www.epicov.org) with both these?
  
  For the moment I could only find:
  
  * [Nextclade's clade definitions](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv)
  * [Pangolin's lineage designations](https://raw.githubusercontent.com/cov-lineages/pango-designation/master/lineages.csv)
  
  What I'm looking for is an annotation as follows:
  
  ```
  lineage    clade
  AY.43      21J 
  AY.4       21J
  ...        ...
  
  ```
  
  The idea is to generate a table as follows:
  
  ```
  genome                                 lineage    clade
  hCoV-19/Germany/BW-RKI-I-195742/2021   AY.43      21J
  ...                                    ...        ...
  
  ```
  
  The way I proceed now is the following:
  
  * Parse the Pangolin's lineage designation file to find a target genome
  * Look for the target genome in Gisaid (for quality check)
  * Parse the metadata associated to the selected genome to get the lineage for verification (only Pangolin lineage is reported)
  
  These steps allow me to build the first part of the table:
  
  ```
  genome                                 lineage    
  hCoV-19/Germany/BW-RKI-I-195742/2021   AY.43      
  ...                                    ...  
  
  ```
  
  Then:
  
  * Paste the genome to Nextclade, wait for the analysis to be completed
  * Report the calculated clade
  
  With this information, I can then build the table:
  
  ```
  genome                                 lineage    clade
  hCoV-19/Germany/BW-RKI-I-195742/2021   AY.43      21J
  ...                                    ...        ...
  
  ```
  
  The idea behind this is that both lineages and clades can be used for "tagging" a genome, depending on the aim (a given clade e.g. 21J includes many lineages e.g. AY.43 and AY.4 in the example above) and that I don't enjoy manual and error-prone procedures;) Thanks for your input.
  
  ---
  
  The GISAID nomenclature via Nextstrain and overall tree is presented [here](https://www.gisaid.org/phylodynamics/global/nextstrain/)
  
  (Crossposted on [Nextstrain's discord forum](https://discussion.nextstrain.org/t/correspondance-of-sars-cov-2-annotations-nextclade-pangolin/883))
  
  **Tags:** phylogenetics, sequence-annotation, covid-19, variants
  
  > **Comments:**
  > **username_1**: The problem is that there's no one to one mapping between pango lineages and Nextstrain clades. One could generate the mapping from the Nextclade reference tree, there most tips have a pango lineage and a Nextstrain clades, and almost all pangos lineages appear in that tree. Other option is to use the open data metadata TSV from Nextstrain, same info.  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_0 on 2021-12-08. Score: 3 | Accepted answer
  
  A comment from a Nextclade's user satisfies my actual needs, I will post it here for future reference:
  
  > Hi - one possible source is the metadata file for UCSC’s daily-updated tree of public SARS-CoV-2 sequences:
  
  ```
  https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/public-latest.metadata.tsv.gz
  
  ```
  
  > It’s a big file – almost 3 million lines – because there are about 3M sequences in GenBank & COG-UK at this point and that number will probably grow. The last two columns of the file (10th & 11th) are the Nextstrain clade and Pango lineage assigned to each sequence based on its placement in the UCSC/UShER tree and the tree’s annotation of where each clade/lineage starts.
  
  > This command will make a file relating each Nextstrain clade to at least one lineage (often to a lot of lineages, especially for Delta):
  
  ```
  gunzip -c public-latest.metadata.tsv.gz | cut -f 10,11 | sort -u > cladeToLineages.tsv
  
  ```
  
  > Some Pango lineages have no public sequences (only GISAID sequences, which can’t be shared at a public URL), so those lineages will be missing from that file. Some older lineages are not monophyletic on the UCSC/UShER tree, so those lineages are not annotated and will be missing. (In total, ~200 / ~1500 are missing.)
  
  
  ---
  
  ### Answer by username_2 on 2022-02-25. Score: 0
  
  Remember not to omit the 'clarification' that in addition to Pango lineages, GISAID clades, Nextstrain clades there is also the WHO nomenclature. We could designate the `Bioinformatics StackExchange monophyly`, surely there is room for one more nomenclature?
  
  Here's the WHO's response copied and uploaded from [here](https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/)
  
  [![enter image description here](https://i.sstatic.net/ovWqZ.jpg)](https://i.sstatic.net/ovWqZ.jpg)
  
  Just to mention NCBI has adopted the Pango lineage nomenclature available on all of its sequences available via [this link](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202%20(SARS-CoV-2),%20taxid:2697049&CollectionDate_dr=1950-01-01T00:00:00Z%20TO%20NOW&CreateDate_dt=1950-01-01T00:00:00Z%20TO%20NOW)
  
  I thought that Omicron was Pango lineage B12, or perhaps B.1.2? Oh I see it has been reclassified following further sequence data.
  
  
  ---
  
  ### Answer by username_1 on 2023-02-13. Score: 0
  
  This information is now easily available in JSON format here: <https://github.com/username_1/pango-sequences/blob/main/data/pango-consensus-sequences_summary.json>. It's one big dictionary of dictionaries with Pango lineage names as outer keys and corresponding Nextstrain clades accessible via inner key:
  
  ```json
  {
   "A": {
    "lineage": "A",
    "nextstrainClade": "19B",
    "nucSubstitutions": [
     "C8782T",
     "T28144C"
    ],
    ...
   },
   "A.1": {
    "lineage": "A.1",
    "unaliased": "A.1",
    "nextstrainClade": "19B",
    ...
   },
   ...
  }
  
  ```
  
  It's straightforward to convert this to a TSV mapping using just minimal scripting.
  
  Beware that not all Pango lineages pre-Omicron are contained therein. Small ones are missing currently.
  
  Disclaimer: I created the repo.
  
  
  ---
  
  