Answers.Body: <p>The obvious thing missing from your list is the <a href="https://www.science.org/doi/10.1126/science.abj6987" rel="nofollow noreferrer">telomere-to-telomere genome assemblies</a> that have been coming out in the last couple years.</p>
  <p>Assembly link <a href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjVuJqem5-CAxV1IDQIHU2mASIQFnoECCQQAQ&amp;url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fassembly%2F11828891&amp;usg=AOvVaw1Q8aP_L5RFstLQ0JtKVX6M&amp;opi=89978449" rel="nofollow noreferrer">here</a>.</p>
  <p>There are now a <a href="https://www.nature.com/articles/s41422-023-00849-5" rel="nofollow noreferrer">few others as well</a> that are similar.</p>
  <p>It's been demonstrated that <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9336181/" rel="nofollow noreferrer">this T2T assembly improves mapping rates</a>, in some cases pretty dramatically.</p>
  <p>I am not sure entirely what you want from whole genome alignments, but UCSC if not others <a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_2395475_t2t-chm13-v1.0&amp;lastVirtModeType=default&amp;lastVirtModeExtraState=&amp;virtModeType=default&amp;virtMode=0&amp;nonVirtPosition=&amp;position=chr22%3A3977324%2D3977530&amp;hgsid=1749469962_FUCnGU4vZLseVNNvfdKfFDr4aeOU" rel="nofollow noreferrer">has incorporated the T2T assembly</a>. <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02735-6" rel="nofollow noreferrer">Here is a related commentary</a> (which I haven't read in any detail).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-31T02:23:52.500Z
Answers.LastActivityDate: 2023-10-31T02:23:52.500Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I found the human genome alignment sets here:
  <a href="https://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html" rel="nofollow noreferrer">https://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html</a></p>
  <p>but they doesn't include, for example, ancient human genomes, e.g. those here:
  <a href="https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data" rel="nofollow noreferrer">https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data</a></p>
  <p>or, for example, any of the other 'pan genome' whole genome alignments here:
  <a href="https://humanpangenome.org/" rel="nofollow noreferrer">https://humanpangenome.org/</a></p>
  <p>However, those latter two resources don't include whole genome alignments...</p>
  <p>About 10 years ago I remember reading a paper that used 'lots' of genomes to uncover novel features using different patterns of conservation, demonstrating the power of the approach.</p>
  <p>Have I missed a new, more up to date, whole genome alignment resource?</p>
  <p>Many thanks,</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-31T04:17:55.307Z
Comments.Text: This seems like it might be an [XY problem](https://en.wikipedia.org/wiki/XY_problem). Can you please provide more context to your question and explain what you want to do with this resource? You're asking for a fairly large dataset, and there's probably a better way to do what you want without downloading all that data.
Comments.UserDisplayName: gringer
Tags: <ensembl><multiple-sequence-alignment><pangenome><whole-genome>
Title: Current 'most comprehensive' whole genome alignment resource for human?
ThreadText: # Current 'most comprehensive' whole genome alignment resource for human?
  
  (Asked by: username_0 on 2023-10-30)
  
  I found the human genome alignment sets here:
  <https://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html>
  
  but they doesn't include, for example, ancient human genomes, e.g. those here:
  <https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data>
  
  or, for example, any of the other 'pan genome' whole genome alignments here:
  <https://humanpangenome.org/>
  
  However, those latter two resources don't include whole genome alignments...
  
  About 10 years ago I remember reading a paper that used 'lots' of genomes to uncover novel features using different patterns of conservation, demonstrating the power of the approach.
  
  Have I missed a new, more up to date, whole genome alignment resource?
  
  Many thanks,
  
  **Tags:** ensembl, multiple-sequence-alignment, pangenome, whole-genome
  
  > **Comments:**
  > **username_1**: This seems like it might be an [XY problem](https://en.wikipedia.org/wiki/XY_problem). Can you please provide more context to your question and explain what you want to do with this resource? You're asking for a fairly large dataset, and there's probably a better way to do what you want without downloading all that data.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-10-31. Score: 2
  
  The obvious thing missing from your list is the [telomere-to-telomere genome assemblies](https://www.science.org/doi/10.1126/science.abj6987) that have been coming out in the last couple years.
  
  Assembly link [here](https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjVuJqem5-CAxV1IDQIHU2mASIQFnoECCQQAQ&url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fassembly%2F11828891&usg=AOvVaw1Q8aP_L5RFstLQ0JtKVX6M&opi=89978449).
  
  There are now a [few others as well](https://www.nature.com/articles/s41422-023-00849-5) that are similar.
  
  It's been demonstrated that [this T2T assembly improves mapping rates](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9336181/), in some cases pretty dramatically.
  
  I am not sure entirely what you want from whole genome alignments, but UCSC if not others [has incorporated the T2T assembly](https://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_2395475_t2t-chm13-v1.0&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr22%3A3977324%2D3977530&hgsid=1749469962_FUCnGU4vZLseVNNvfdKfFDr4aeOU). [Here is a related commentary](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02735-6) (which I haven't read in any detail).
  
  
  ---
  
  