Answers.Body: <p>This is one of the primary use cases for which spacegraphcats (<a href="https://www.biorxiv.org/content/10.1101/462788v2" rel="nofollow noreferrer">preprint</a> and <a href="https://github.com/spacegraphcats/spacegraphcats" rel="nofollow noreferrer">code</a>) was designed. The "neighborhood queries" discussed in the paper sound particularly relevant. I don't have any personal experience with spacegraphcats, but the <a href="https://github.com/spacegraphcats/spacegraphcats/blob/master/doc/running-spacegraphcats.md" rel="nofollow noreferrer">run guide</a> provides some examples of how to index the complete data set and how to query sequences of interest.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-09T17:58:31.013Z
Answers.Text: Yes, we'd be happy to chat (I'm one of the spacegraphcats authors). Just post questions over on our github repo!
Answers.UserDisplayName: Titus Brown
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-09T17:58:39.067Z
Answers.Text: You might also be interested in citations 21 and 22 in the spacegraphcats paper - metacherchant and a paper that does something similar.
Answers.UserDisplayName: Titus Brown
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-09T16:18:30.580Z
Answers.LastActivityDate: 2019-04-09T16:18:30.580Z
Answers.UserDisplayName: Daniel Standage
Body: <p>My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic region. </p>
  
  <p>Is there a way I could assemble only sequences that create a contig which contains my region of interest? Contigs which don't contain this region are not useful to me. My organism of interest might represent a minority of the metagenome, and assembling everything in the dataset would use a lot of computing power.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-09T11:57:52.897Z
Comments.Text: Good question! I know that some of the assemblers for mtDNA are working on this principle - searching for reads mapping to a conserved mt gene and then extending the sequence, maybe you could tweak one of those tools.
Comments.UserDisplayName: Kamil S Jaron
Tags: <phylogenetics><fasta><assembly><metagenome>
Title: Is there a way to assemble contigs starting from a specific sequence?
ThreadText: # Is there a way to assemble contigs starting from a specific sequence?
  
  (Asked by: username_0 on 2019-04-09)
  
  My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic region.
  
  Is there a way I could assemble only sequences that create a contig which contains my region of interest? Contigs which don't contain this region are not useful to me. My organism of interest might represent a minority of the metagenome, and assembling everything in the dataset would use a lot of computing power.
  
  **Tags:** phylogenetics, fasta, assembly, metagenome
  
  > **Comments:**
  > **username_1**: Good question! I know that some of the assemblers for mtDNA are working on this principle - searching for reads mapping to a conserved mt gene and then extending the sequence, maybe you could tweak one of those tools.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2019-04-09. Score: 2 | Accepted answer
  
  This is one of the primary use cases for which spacegraphcats ([preprint](https://www.biorxiv.org/content/10.1101/462788v2) and [code](https://github.com/spacegraphcats/spacegraphcats)) was designed. The "neighborhood queries" discussed in the paper sound particularly relevant. I don't have any personal experience with spacegraphcats, but the [run guide](https://github.com/spacegraphcats/spacegraphcats/blob/master/doc/running-spacegraphcats.md) provides some examples of how to index the complete data set and how to query sequences of interest.
  
  > **Comments:**
  > **username_3**: Yes, we'd be happy to chat (I'm one of the spacegraphcats authors). Just post questions over on our github repo!  
  > **username_3**: You might also be interested in citations 21 and 22 in the spacegraphcats paper - metacherchant and a paper that does something similar.  
  
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