Answers.Body: <p>That's a good question. I remember seeing a poster about making trees directly from reads, but unfortunately, I can not find any other record than this <a href="https://twitter.com/ISBSIB/status/1011987705507516416/photo/1" rel="nofollow noreferrer">tweet</a>. Perhaps you can try to email David, if he would be keen to share the implementation. </p>
  
  <p>While searching for any information about David's work, I run into a GitHub repository called <a href="https://github.com/kheyduk/reads2trees" rel="nofollow noreferrer">reads2trees</a>. It's quite old and it's not super popular, so hard to say if it can be useful. But the name matches the problem description quite well.</p>
  
  <p>I also remember there were some attempts (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224691/" rel="nofollow noreferrer">An example paper</a>) to get phylogeny directly from kmers, but I have never tried that on my own. I also think these approached were focused on microbial phylogienies. So again, not sure if it's going to be useful for you.</p>
  
  <p>That's all I got.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-27T09:22:43.260Z
Answers.Text: The "reads2trees" techniques should be able to give you sequences too (it's just a fancy name for a special case of reference-based assembly anyway). The kmer-based methods certainly won't. Good luck
Answers.UserDisplayName: Kamil S Jaron
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-25T08:36:35.940Z
Answers.Text: Thank you very much for your suggestions! I'm going to check that, however the ideal for me would be to retrieve the sequences not just the phylogenetic tree, for example to do selection analysis.
Answers.UserDisplayName: LauraR
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Answers.CreationDate: 2020-04-24T13:53:44.040Z
Answers.LastActivityDate: 2020-04-24T13:53:44.040Z
Answers.UserDisplayName: Kamil S Jaron
Body: <p>I have a lot of unassembled sequencing data and I want to build phylogeny for some genes from these data. I can retrieved the sequene by mapping reads to a reference sequence but if the two species are too divergent, reads will not match and I won't get the full CDS. Is there a better way to deal with that? Maybe I can do that to retrieve the well conserved part and then extend this region with reads that overlap (as if it was gap-filling)? 
  What do you think of this approach? Do you know a software for such extension process? 
  Thanks</p>
  
Tags: <gene><assembly><read-mapping><phylogeny>
Title: Assemble reads for a specific gene
ThreadText: # Assemble reads for a specific gene
  
  (Asked by: username_0 on 2020-04-24)
  
  I have a lot of unassembled sequencing data and I want to build phylogeny for some genes from these data. I can retrieved the sequene by mapping reads to a reference sequence but if the two species are too divergent, reads will not match and I won't get the full CDS. Is there a better way to deal with that? Maybe I can do that to retrieve the well conserved part and then extend this region with reads that overlap (as if it was gap-filling)?
  What do you think of this approach? Do you know a software for such extension process?
  Thanks
  
  **Tags:** gene, assembly, read-mapping, phylogeny
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-04-24. Score: 2
  
  That's a good question. I remember seeing a poster about making trees directly from reads, but unfortunately, I can not find any other record than this [tweet](https://twitter.com/ISBSIB/status/1011987705507516416/photo/1). Perhaps you can try to email David, if he would be keen to share the implementation.
  
  While searching for any information about David's work, I run into a GitHub repository called [reads2trees](https://github.com/kheyduk/reads2trees). It's quite old and it's not super popular, so hard to say if it can be useful. But the name matches the problem description quite well.
  
  I also remember there were some attempts ([An example paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224691/)) to get phylogeny directly from kmers, but I have never tried that on my own. I also think these approached were focused on microbial phylogienies. So again, not sure if it's going to be useful for you.
  
  That's all I got.
  
  > **Comments:**
  > **username_0**: Thank you very much for your suggestions! I'm going to check that, however the ideal for me would be to retrieve the sequences not just the phylogenetic tree, for example to do selection analysis.  
  > **username_1**: The "reads2trees" techniques should be able to give you sequences too (it's just a fancy name for a special case of reference-based assembly anyway). The kmer-based methods certainly won't. Good luck  
  
  ---
  
  